Performance Reviews
by LMXB
Summary: All ready exhausted, Jennifer and the others are subjected to the IOA latest scheme, during which things go wrong. No pairings to start with but there will eventually be a Ronon/Jennifer flavour to the story.
1. Chapter 1

**Summary: **All ready exhausted, Jennifer and the others are subjected to the IOA's latest scheme, during which things go wrong. No pairings to start with but there will eventually be a Ronon/Jennifer flavour to the story.

**Disclaimer: **I don't own any of the characters or background IP. All writing is for fun.

**A/N: **The inspiration for this originated from a theme that came from daisyscrapper's last story, 'Never the Same'

* * *

"Welcome back." Woolsey greeted as Lorne's team came through the Gate. "Ahead of schedule and unscathed." Woolsey commented, glancing a look at Jennifer, making sure the doctor had remained trouble free.

"What can I say? My team isn't attention seeking." Lorne grinned.

"Did everything go as planned?" Woolsey asked, directing his question at Jennifer.

"They are all making good progress. I'd like to go back in a week just to check that there are no unexpected consequences. But based on what we saw, I'm confident they'll all make a full recovery." Jennifer replied. Noticing her weariness Woolsey said.

"I'm sure that you want nothing more than to get some sleep, however, something has come up and I need you at a meeting in thirty minutes."

"Can't it wait?" Lorne asked, concerned for Jennifer.

"I'm afraid not. I've delayed the announcement, as it is, until Dr Keller was back. It won't take long, but I'd like you to hear it first hand."

"That doesn't sound good." Lorne stated, voicing what Jennifer was thinking.

"It's nothing to worry about." Woolsey assured them. "I'll explain everything in the briefing. To give the rest of you some time, we'll hold the mission debriefing tomorrow." With that he turned and headed back to his office.

"Cheer up." Lorne said to Jennifer, "he said it was nothing to worry about."

"But on whose scale?" Jennifer asked.

"You need to relax doc. Perhaps an uneventful mission is a good omen." Lorne smiled as they walked down to the infirmary.

"Or perhaps the cosmic scale will now need rebalancing." Jennifer groaned.

-00-

Nearly thirty minutes later an exhausted Jennifer climbed the stairs to the briefing room, almost too tired to care about the announcement. As she entered she smiled at those already there before sitting in the spare seat next to Rodney who commented.

"Wow, you look terrible."

"Thanks Rodney." Jennifer threw back.

"I thought you were going to take some time off?" Teyla said.

"I was, but we're short staffed in the infirmary. And the flu is still taking its toll. So I'm having to fill the gaps."

"At least reinforcements will be here soon." John said, referring to the imminent arrival of the Daedalus.

"Not for the infirmary." Jennifer said, unable to hide her frustration.

"I thought you'd requested more staff?" John said.

"I had, but it was turned down. Again."

"Why?"

"Budget cuts. We only fix people, so are a secondary concern." Jennifer replied.

"That's bu-"

"Good Evening everyone." Woolsey said hurrying into the room. "I won't keep you long." As he sat he noticed John, Ronon and Teyla sitting round the table and commented. "As much as I appreciate your enthusiasm there is no need for you to be here."

"Excellent, I'll go." Rodney said standing.

"Not you Dr McKay. I was talking to Colonel Sheppard, Ronon and Teyla. How did you even find out about this meeting?"

"Lorne mentioned it. I assumed my invite got lost." John said suddenly feeling suspicious.

"There was no invite. This meeting is regarding policies affecting civilian groups only." Woolsey tried to explain. Sensing John's suspicion though he added. "You are of course welcome to stay if you wish."

"Okay." John agreed, relaxing slightly. Teyla and Ronon remained in their seats following John's lead.

"If they are staying, couldn't they just take my place?" Rodney asked hopefully.

"No. This announcement will have an impact on you."

"That sounds bad." Rodney replied.

"It is not bad. We can use this to our advantage." Woolsey assured him.

"That sounds really bad." McKay countered.

"Perhaps you should let Mr Woolsey make the announcement before jumping to conclusions." Teyla suggested, curious as to what the announcement was.

"Thank you Teyla." Woolsey said, nodding his gratitude. "As you know it has been six months since the last performance reviews and as such it is time for another round." Holding his hand up to mute the grumbling he went on. "This is an important task, not just a paperwork exercise. That means, Dr McKay, that all heads of staff must take responsibility for all the appraisals."

"Why are you singling me out?" Rodney asked before pointing to John and adding, "he did just as many as me last time."

"I think you'll find that Colonel Sheppard did actually add a few words to Major Lorne's appraisal, even though the Major wrote most of it, you didn't even read Zelenka's one." Woolsey said. "There will be some changes this time though. The IOA are concerned that whilst the department heads are appraising those who work under them, there is no one qualified checking the work of the heads. As such they cannot make educated decisions about the status of the expedition. So the IOA want to ensure the right people are doing the appraisals of the senior staff. As such all of your appraisals will be carried out by independent experts in your fields."

"Rubbish." McKay muttered. "If they were experts they would be involved in the expedition and not independent. Besides who knows more than I do about theoretical and practical Ancient Tech?"

"Carter for one." John shot back.

"It is not just about your knowledge, it is how you are running your departments and your people." Woolsey said quickly, wanting to stop the potential bickering between Sheppard and McKay before it started.

"Are we going to have to go back to Earth for the review?" Jennifer asked.

"No. The IOA realise that what we do is unique in nature, so will be sending the representatives here. They will shadow you for ten days before carrying out your appraisal report. During the ten days they will, hopefully, get up to speed about the role and the working conditions thereby they should understand the full complexities of what we have to go through."

"How exactly can we use this to our advantage?" Rodney asked. "It sounds like we'll have to lose at least ten days of valuable time."

"Currently the IOA and SGC are under extreme pressure to cut budgets. This is done by cutting supplies and manpower. They do it because they don't really think we need the extra resources as they are basing their decisions on Earth based scenarios. If we can prove to these independent assessors that what we do is different enough they may start to push for more money on our behalf."

"That's a lot of 'ifs' and 'mays'." John pointed out.

"True, but that's all we've got." Woolsey said. "To help you I have managed, with the help of General Landry, to get some information on each of the experts being sent. I think the best course of action is to learn about them and figure out what they'd expect to see. Regardless of our feelings this will be happening. Let's try to work with the system to change the system."

"So when do they come?" McKay asked.

"They arrive with the Daedalus in two days."

"Two days?" Jennifer asked suddenly waking up. "That doesn't leave much time."

"No it doesn't." Woolsey agreed. "So I suggest you all go and prepare."

* * *

**A/N: **Next chapter up as soon as possible.


	2. Chapter 2

"Hey doc." Lorne greeted as he strolled into the infirmary.

"Hey." Jennifer replied distractedly as she counted boxes.

"What are you doing?" Lorne asked scrunching his eyebrows.

"Stock taking." Jennifer said as she scribbled something down.

"I thought that was a monthly activity?"

"Uh-huh."

"Then why are you doing it, again? You have stocktaked, if that is even a word, every evening this week. Are you really that worried about this performance review?" The Major asked as he walked over to Jennifer, who reluctantly turned to face him. As he saw the dark rings under her eyes he assured her. "It'll be fine. What can he complain about?"

"Everything." Jennifer said dejectedly.

"That's a little overdramatic isn't it?"

"You should see his file. He's the type of person who should be running the infirmary. He spent years running clinics in various parts of Africa, dealing with unusual diseases, poor conditions and a budget that makes a shoestring budget look generous. He's experienced, well liked, moves in the right circles, is well known and a brilliant doctor. He's going to tear me to pieces."

"Hey. There is only one person who should be running the infirmary here and she already has that job. Besides there is a big difference between dealing with malnourished children and underfed Wraith." Lorne said, trying to boost Jennifer's confidence. "But if you really are that worried, go back to basics. Remember first impressions count." Noticing Jennifer's confused face he added. "You look like you haven't slept in weeks. Is that the impression you want to give?"

"No."

"Then get some rest. Things will look better in the morning."

"I doubt it." Jennifer replied. "Besides I'm not tired."

"Doc you can either wait in your room and worry for the next ten hours or you can go to your room and sleep. Either way you are going to your room." Lorne said forcibly.

"Fine, but if he complains about the poor inventory I'm holding you responsible." Jennifer said giving up.

-00-

The following day Jennifer nervously stood outside the control room, waiting for the IOA man to emerge from his briefing with Woolsey. As time ticked by she grew more and more nervous, remembering how she felt when she was a med student on rounds. Finally the doors opened and Jennifer got her first glance of the man she needed to impress.

"Dr Keller, I'm Dr John Hamilton." A man in his early fifties said as he firmly shook Jennifer's hand.

"Dr Hamilton." Jennifer replied. "Where would you like to start?"

"I'm just here to observe. I do not plan on interacting directly with anyone other than yourself and even that's on a as needed basis. I'll just shadow you, please ignore me."

"You don't want a briefing first?" Jennifer asked, unsure if his approach was good or bad.

"That won't be necessary. I'll pick up everything I need as time goes on."

"As you wish. I'll take yo-" She started only to be cut of by Hamilton.

"No explanations please. Just pretend I'm not here." Raising her eyebrow in surprise Jennifer turned and started to walk silently to the infirmary.

-00-

"Dr McKay. I'm Giles Milton." A middle aged, smartly dressed man greeted stepping into Rodney's lab.

"I know. Woolsey showed me your file." Rodney said, without looking up from his screen.

"Good. So you'll know I have a backgr-"

"No offence but your background is irrelevant." Rodney said. "You are here to fill in some paperwork. You and I both know I won't be removed from the project. So if you don't mind I'm busy trying to save the Galaxy." When no argument was voiced Rodney thought he'd won the argument that was until a hand reached out and snapped his laptop shut.

"I see your arrogance was not exaggerated." Milton stated. "While I may not be able to send you to a cold and remote outpost, I can have you demoted. I'm sure Dr Zelenka would like a chance to flex his managerial muscles."

"Don't make me laugh." Rodney shot back. However, on seeing Milton's steely expression the physicist started to get worried.

"Believe me Dr McKay, demotion is only the start of what I can do. So let's start, where are you log books?"

"Log books?"

"Yes your log books, where you note your progress."

"All reports are typed and submitted to the SGC and IOA."

"I didn't ask about the reports, I want your notes, detailing exactly what you have done."

"Everything important is in the reports. Everything else is in my head."

"Who gives you the right to decide what is important?"

"The IOA, when I was put in charge." Rodney said smugly.

"For this exercise they have put me in charge so I suggest you start cooperating fully. Let's start with this galaxy's version of the replicators."

-00-

At the end of the day Jennifer found herself sitting in the Mess Hall playing with her food. She was so lost in thought she didn't even register Teyla was talking to her until the Athosian shook her shoulder.

"Teyla!" Jennifer exclaimed. "Sorry I was miles away."

"I noticed." Teyla smiled. "Do you mind if I join you?"

"Of course not."

As Teyla sat Jennifer subconsciously went back to playing with her food.

"Food is normally better eaten rather than played with." The Athosian pointed out.

"I'm not very hungry." Jennifer said pushing the plate to one side.

"The IOA thing going that well?" John asked as he sat down next to Teyla.

"How'd you guess?" Jennifer said miserably.

"It's a sixth sense." John shrugged. "I have to say I'm surprised to see you here. I haven't seen you eat here for days, not since before the flu outbreak."

"Too busy working."

"So that does mean that your workload has eased?" John asked.

"I wish. I just can't cope with Hamilton standing behind me writing notes. I'll go back later."

"Think of it this way, in under two weeks time he'll be gone." John said.

"If the quantity of notes he is taking is anything to go by, so will I." Jennifer said sadly. Before John or Teyla could follow up on the comment they were interrupted by Rodney dropping his tray on the table ranting.

"That arrogant, self serving, egotistical, obnoxious son of a –"

"Have you looked in a mirror again?" John asked, trying to lighten the mood.

"Not funny." McKay replied. "I swear I'm going to do something he may regret. Who does he think he's talking to? If it weren't for me Earth would probably have been harvested by the Wraith. Do I get thanks, no. I get Milton. They could have at least sent a real physicist."

"A real physicist?" John questioned. "I thought he was a physicist."

"Please. He wears a suit. No self respecting scientist would wear a suit to work." Looking over to Jennifer he asked. "Why are you looking so glum? I hear yours doesn't even talk to you."

"He just follows me round noting down all my deficiencies." Jennifer replied.

"I'm sure it can't be that bad." John said.

"Really? Ask Lorne tomorrow after the mission."

"What mission?" Rodney asked.

"P39 – 3FX. We're checking to see how they are recovering from the flu."

"Can I come?" Rodney asked hopefully.

"You want to go on a humanitarian trip?" John asked doubtfully.

"If I go Milton goes and terrible things can happen off-world." Rodney explained.

"Sometimes you scare me." John said as Jennifer stood.

"Well hopefully my shadow has gone so I'm going to get some work done."

"Make sure you get some rest doc." John ordered, worried she looked so tired.

"When I can, I will." Jennifer said walking off.

Looking at Teyla John commented. "This is going to be a fun few days."


	3. Chapter 3

Jennifer stormed into the gym desperate to take her anger and frustration out on something that wasn't going to get her sacked. As she entered though she nearly groaned as she saw the sole occupant was Ronon.

"Doc." He greeted coolly.

"Ronon." Jennifer replied. "Sorry, I didn't realise you were in here. I'll go."

"Wait." He called before she could turn. Obediently Jennifer remained in position and waited for Ronon to say what was on his mind. She continued to wait as the Satedan searched for the right words. When none came she continued to wait until she was overwhelmed by the awkwardness. She was just devising a polite escape strategy when Ronon offered.

"You want to spar?"

"With you?" Jennifer blurted out.

"It's been a while since you've trained. You can practice against me." Ronon offered before adding. "You look like you need it."

"You have no idea." Jennifer said, glad she was managing to have a conversation with Ronon again.

"You want to talk about it?"

"Seeing what I want to do is murder him I don't think talking will cut it." Jennifer said, forcing a smile.

"Murder who?"

"Hamilton."

"The IOA guy?" Ronon asked, throwing Jennifer a stick.

"The IOA guy." Jennifer confirmed.

"What's he done?" Ronon questioned, curious at what had got Jennifer so riled.

"Imagine Rodney, without the good points. Increase his arrogance and decrease his self awareness –"

"Not sure that's possible doc." Ronon said.

"Trust me, it is. Hamilton is the living proof."

"I thought he didn't talk to you." Ronon said as he fended off some swings from Jennifer.

"That was yesterday. Apparently he grew bored of not talking about himself so today he has told me all about himself and how he would be doing things differently. If I hear the phrase 'back when I was in' one more time I think I'm going to lose it. It wouldn't be so bad if every so often something he said was medically relevant, but so far not one piece of useful information has crossed his lips."

"He'll be gone soon." Ronon said as he started to carefully launch his own slow blows, all of which Jennifer defended.

"Soon isn't soon enough." Jennifer complained as she countered. This time as she put all of her frustrations into the blow she overbalanced and ended up in a heap on the floor.

"Don't over stretch yourself." Ronon chastised.

"Wasn't deliberate." Jennifer mumbled as she clambered to her feet again, starting to feel the tiredness take over.

"Concentrate on what's happening here. Not the IOA guy." Ronon said causing Jennifer to say.

"Easier said than done."

"Try." Ronon said firmly as he started another sequence of strikes, this time quicker. As he made his moves he was concerned with how slow Jennifer's reactions were and at one point nearly struck her head when she failed to defend herself.

"You okay?" He asked.

"Just tired. I should call it a night. I'll leave you to it." Jennifer said backing away.

"I've got to go anyway. I'm due on the Daedalus soon."

"You are?" Jennifer asked surprised.

"Yeah. McKay is showing his IOA guy some event in another system. Whole team has to go." Ronon shrugged.

"Enjoy."

"Doubt I will. It's going to be dull."

"Dull is better than a Wraith attack." Jennifer pointed out.

"If you say so."

"Ronon." Jennifer called as the Satedan reached the door. "I know things have been weird, but thanks for tonight. I needed it."

"Anytime doc." Ronon said leaving Jennifer alone in the gym.

-00-

"You have a minute?" John asked as he entered Woolsey's office.

"Of course. But I thought you were about to leave."

"Not for fifteen minutes, this shouldn't take that long." John explained as he shut the door.

"Take a seat." Woolsey suggested as he closed his folder.

"Where's your IOA shadow?" John questioned, wanting to make sure they weren't about to get interrupted.

"Getting some food. She won't be back for some time." Woolsey assured him.

"Good. I jump straight to it. This IOA visit is having negative effects on everyone."

"You mean Dr McKay?"

"As an example, but it is not just Rodney. Keller as well is getting wound up. Lorne was not complimentary about Hamilton's behaviour towards her on the mission. We've been pushing her too had recently as it is. The last thing she needs is this."

"What would you have me do?"

"Get rid of them." John suggested only half joking.

"Colonel, regular appraisals of performance is a key part of the IOA's role. They will not just scrap it as you don't approve."

"It's not that I don't approve, it is just that I don't think we need all the regulations. If you say McKay does a good job, that should be enough. Too many regs don't help anyone."

"Regulations are there for a reason." Woolsey said. "We need rules and regulations to function safely and effectively."

"True, but not every aspect of life needs them. A child lives quite happily without them." John countered.

"Although it does feel at times like I am overseeing several arguing children, you are all in fact adults. Besides any child who has been read the three little pigs has some appreciation for the need for regulations." Woolsey said.

"The three little pigs?" John asked, convinced that one of them had lost their mind.

"Yes, it is a story about th-"

"I know the story, I just don't see the link."

"It's simple. The first two pigs showed no regard for hard work and ended up with substandard houses. The third, built a real house, adhering to proper regulations, unafraid of the extra work. As a result, he was safe. The message is clear, if you don't follow regulations you risk getting eaten by a monster, in the pigs' case a wolf. Follow regulations and you will remain safe."

"So the IOA is a monster?" John asked, glad that Woolsey hadn't been around to read him bedtime stories as a child.

"That's not what I said." Woolsey replied. "The point is, the visit may be taxing and drain resources and cause some turbulence, but at the end of the day these reviews are for all of our protection and will ultimately result in a city operating in a more efficient way."

"I hope you're right, I really do. But if there isn't a change of attitude we are going to have some very disgruntled scientists on our hands." John warned.

"I understand and I'll do all I can." Woolsey assured him.


	4. Chapter 4

As Jennifer released another marine from the infirmary she turned to see Hamilton furiously scribbling down notes.

When he finally looked up and saw Jennifer stare at him he said.

"I know I am meant to hold all feedback until day ten, however, I think this is too important to ignore."

Jennifer slowly counted to ten in her head, wondering what was awaiting her on day ten if his constant criticism was not viewed as feedback.

"Let's go to your office." Restarting her count she followed him to her office and shut the door. No sooner as it had shut he started.

"This again is down to your lack of experience and is something that should have been caught earlier. You are far too friendly with the patients. You have to become more detached. When I was in Kenya running the infirmaries at various camps there were many, many, interesting char…."

As Hamilton once again launched into a story about his past Jennifer, already exhausted, could feel her eyes glaze over. As she carefully tried to give some well placed nods she started thinking about what had to be done over the next few days. She then went on to think about one of the brain teasers Lorne had told her a few days ago. Having solved that she tried to remember what Sheppard had taught her about stances when shooting. Just as she was concerned she was running out of things to say the general alarm sounded. Tensing she reached to her radio just as Woolsey gave a city wide announcement.

"The Wraith are in orbit and starting attack runs. Everyone initiate operation Gamma. This is not a drill. I repeat this is not a drill." As if for emphasis moments later the infirmary shook as a Wraith bombardment hit the shields. Forgetting about Hamilton Jennifer ran out and started issuing orders to the staff already there and the staff who were sprinting into the infirmary. When she was content everyone knew what to do she went to set up several ORs, hoping she wouldn't need them.

When she finished she stepped back out into the main infirmary, pleased to see everyone operating in a calm, professional way. She was going to ask Woolsey for an update when two marines jogged into the infirmary holding a large trunk between them.

"Dr Keller." One of them said. His large frame a stark contrast to Jennifer's petite figure. "Major Lorne has assigned us to guard the infirmary. We'll take up position in the corridor and try to keep out of your way. But if you need us shout."

"Thank you Captain." Jennifer replied, reassured they had some protection.

"The Major has also ordered everyone who is trained to carry a sidearm." He added opening the trunk, revealing a small weapons cache. "You are first on the list."

Not wasting time arguing Jennifer took a gun and a holster. Once it was clipped round her waist she nodded to the Captain to issue the rest of the weapons. Turning she almost walked straight into Hamilton who asked, in almost disbelief.

"You are wearing a gun? In the infirmary?"

"We're under attack." Jennifer pointed out as she attempted to side step him.

"You're a doctor not a soldier." Hamilton said gripping her arm.

"Sometimes, here, you have to be both. Please excuse me I need to-"

She was cut off by a huge tremor and the lights going out. Moments later they flashed back into life just as Woolsey radioed.

"Be advised we have lost shields to various parts of the city. The Wraith are breaching. I repeat, the Wraith are in the city."

"How is that possible?" A pale Hamilton asked. Jennifer did not have time to answer though as seconds later the first casualties started to arrive.

-00-

Jennifer wasn't entirely sure how much time had passed since the original alarm, but the casualties were mounting and space as well as her energy was running out. Knowing there was no other choice she started to order half her staff to the gym where they were to set up a triage centre for the walking wounded. Just as she was assigning teams she heard a voice she had forgotten about in the chaos.

"Dr Keller," the still pale Hamilton said, "I really must intervene, you are doing this all wrong. This is not the-"

"Dr Hamilton." Jennifer interrupted, unable to keep her temper in check any longer. "You are here to observe and learn about conditions here, not to interfere. If you don't like the way I'm doing something write a report. Now is not the time to raise concerns. Either stay out of my way or help out, following whatever orders you are given regardless of whether you agree." Not waiting for his response Jennifer turned back to her staff and issued them with instructions. As they left the infirmary taking the walking wounded with them she started to feel like she had everything under control. She even considered sitting down for a few minutes. That was until she received a message she dreaded.

"Dr Keller." Woolsey said, his tone grim. "Major Lorne has been injured on an offensive against the hive. His team are bringing him back now, he's in a bad way."

As her heart plummeted she replied. "I'll meet them at the Jumper bay."

"Negative." Woolsey said. "The corridors are crawling with Wraith and we can't spare an escort. Lorne's team will bring the Major to you. As soon as we are able we'll patch his team through to you so you know what to expect."

"Understood." Jennifer said, trying to fight the helpless feeling. "I'll prepare things down here."

For the next ten minutes Jennifer rushed round the infirmary, planning for every contingency. When she was finally able to speak to Lorne's team, who described the Major's injury, she prepped the operating theatre wanting to make sure she was ready the second they made it to the infirmary. Once everything was set up time dragged as she waited and waited.

When Lorne was finally carried into the infirmary she was momentarily stunned by how pale he was and the amount of blood that covered him. Ordering Lorne's team to place him on a gurney she quickly inspected the damage before rolling him into surgery calling over to her nurse to find as much O Neg as possible.


	5. Chapter 5

For the next six hours Jennifer and her small surgical team fought to save Lorne. In the background the power continued to be unreliable and the city continued to shake. Several hours into the surgery, if she hadn't been so focused on Lorne she may have noticed the barrage ease up, then stop. Instead her attention was locked on the Major who hovered between life and death.

When she was convinced that he was finally stable she stepped back from the table and allowed herself to relax momentarily. She took a deep breath and ran through a mental checklist. Happy she had covered everything she looked to Marie and said. "I want him under constant observation."

"Understood doctor." The nurse replied.

Content everything was under control Jennifer removed her gloves and apron before setting foot in the main infirmary. Looking round she saw her team efficiently treat the seriously wounded. Seeing she was temporarily surplus to requirements she allowed herself a deep breath and reached for her radio so she could report in.

"Go ahead Dr Keller." Woolsey's strained voice said.

"Lorne is stable. What's the situation out there?"

"That's good news." Woolsey said relieved. "The Hive is down, but there are still groups of Wraith in the city. Scanners are down so we don't know where. For now you are to remain in the infirmary."

"I doubt that'll be an issue." Jennifer said moments before she heard gunfire from the corridor. "I think we're under attack." She said quickly. "There is gun- The Wraith are here." She announced as she saw two Wraith enter the infirmary firing at all who stood in their way. Ignoring Woolsey's request for more information she watched those who could dive for cover, whilst others tried to shield their patients. Then just as one Wraith fell to his knees the other approached Hamilton, who stood paralysed with fear in the corner. Her staff, busy with their battles to heal the critically wounded were unable to intervene giving the Wraith enough time to rip open Hamilton's shirt and raise its feeding hand. Instinctively Jennifer reached for her 9 mil and carefully aimed at the Wraith, getting off a shot before it could feed. As the bullet hit the Wraith it turned to look at Jennifer and snarled. Temporarily forgetting about Hamilton the Wraith approached Jennifer who emptied her clip into the Wraith's chest. The bullets however had no affect and the Wraith kept coming. When it was within striking distance it unleashed a blow knocking Jennifer to the floor. Content that the gun was out of her reach he knelt down and raised his hand to feed only to be propelled back by several rounds of P90 fire going through his chest.

As much as Jennifer want to sit up and see what was happening the shout of 'Stay down' and gunfire was enough to keep her frozen in position and out of the way of the cross fire. Finally she saw a pair of standard issue boots near a head before Teldy said.

"Its clear." The major offered Jennifer a hand and helped the doctor get back to her feet.

"Thanks." Jennifer replied as she saw the captain who had been guarding the infirmary be carried in. Forgetting the Major she ran over to his side to assess the damage. Dismayed to see several Wraith blasts had burnt through his torso she ordered him to be taken to surgery where she and her small team tried to bring Astil back to the land of the living. This time though the damage was to great and when he flat-lined there was no way back.

Knowing there was nothing more she could do Jennifer shook her head and called the time of death. Ripping off her gloves she left the OR and went into her office, to give herself thirty seconds to collect her thoughts. However, before she could shut the door Hamilton was pushing himself inside. Turning on him, too upset to keep her emotions in check she said.

"If you are about to lecture me on getting too emotionally involved with my patients, now is not the time." Not giving him a chance to respond she stormed out of the office and went over to assist Cole.

-00—

The bridge crew all watched McKay and Milton have another blazing argument before they disappeared to the shield generator room. As peace returned to the bridge Caldwell looked at Sheppard and said.

"You know I'm actually feeling sorry for McKay."

"Don't let him hear you say that." John quipped. Although he too was concerned about McKay and the treatment he was receiving.

"Um Sir, we may have a problem." Marks said looking up from his console.

"What type of a problem?" Caldwell questioned.

"I can't reach Atlantis."

"Dr McKay warned that would be an issue due to the storm." Caldwell pointed out.

"Yes Sir, that was true yesterday, but the storm has subsided and the incoming flux is low enough that we should be able to reach Atlantis and hear their reply."

"You sure?" Sheppard asked.

"Yes Sir. I have double checked the calculations." Marks replied confidently. Glancing at Caldwell John grabbed his radio and ordered.

"McKay get to the bridge."

"Can't it wait?" Was the delayed but almost inevitable reply.

"No it can't doctor." Caldwell cut in causing McKay to agree.

"I'm on my way."

Two minutes later McKay and Milton reached the bridge, McKay immediately asking.

"What's the problem and couldn't you have mentioned it before I left?"

"We can't reach Atlantis." John said.

"That's odd." McKay agreed walking over to a console. "It could be the extra flux damaged our comms array." He suggested.

"I thought you said there would be no danger of damage." Milton said.

"I said there was a low risk of damage." McKay countered, clearly at the end of his tether.

"It appears the risk was higher than you anticipated." Milton shot back only for Marks to interrupt.

"Actually all tests came back okay. Our array is working fine."

"Could your experiments have caused any other damage?" Milton continued to accuse.

"No." Rodney said confidently as he continued to type at the console. Eventually he turned to John and said. "The problem is definitely not this end."

Without missing a beat Caldwell ordered. "Lay in a course for Atlantis."


	6. Chapter 6

"Colonel Sheppard." Major Teldy greeted as John's team beamed back into the control room.

"What the hell happened?" John asked as he saw the carnage.

"The Wraith. They appeared approximately forty hours ago and attacked the city. The shields did not last long and when they were taken out so were comms and sensors. They then started to enter the city. Major Lorne launched an offensive to take down the Hive. It worked, but he's injured, badly. We think we've got all the Wraith who invaded, but there may still be pockets not found yet."

"McKay?" John barked.

"I'll get the sensors working." The physicist said jogging off.

"How did they find us?" John asked.

"We told them. That is to say a beacon was activated in one of the new labs. They must have used it as a homing device. It is now deactivated." She added. "Dr Zelenka is looking into how it got activated."

"Any other Wraith coming?" John asked.

"Unknown, our long range sensors are also down. But we've not been attacked again so maybe we're okay. Now the Daedalus is here though we should be able to get an idea of the situation using her sensors."

"What else do I need to know?" John questioned.

"We've lost seven in the fire fights. Six in combat, one who didn't pull through surgery. Another seventy-three are injured and unfit for duty. The infirmary is swamped and we don't have the manpower to fend off another attack."

"Liaise with the Daedalus and borrow some of their marines to make up numbers. I want every inch of the city searched for Wraith, traps and everything else you can think of."

"Yes Sir."

John was about to give another order when he realised someone was missing.

"Where's Woolsey?"

"Infirmary."

"How bad?" The Colonel asked, knowing the city couldn't lose another leader.

"He's fine." Teldy answered. "Well shaken, but uninjured. He went down to assess the damage down there. It was one of the scenes of a firefight. He asked that if you turned up you come down to see him." The Major explained, before looking at the remainders of his team and adding. "Teyla, Ronon, I could use you on the sweep."

"Of course." Teyla replied immediately. "Where do you want us?"

"Pier 15." Teldy responded. Without saying a word Ronon turned and ran off, closely followed by the Athosian.

"Continue bringing order to this mess." John said looking at the exhausted Major. "I'm going to see Woolsey."

"Yes Sir." Teldy responded, glad to have back up at last. Before John left the gate room she called. "Sir, be careful there could be Wraith between here and the infirmary."

"Understood." John called as he left the safety of the gateroom and jogged towards the infirmary, surprised and dismayed by the amount of damage that had been done to his home. Although he still wasn't clear how exactly this could have happened he did know it would take a long time to recover.

When he finally reached the infirmary he was surprised by the level of calmness in the area. A calmness that was in stark contrast to the scarred walls, exposed circuitry and flickering lights. He scanned the room and saw many of his people lying unconscious seemingly oblivious to the carnage that was still going on in the city. Seeing Woolsey and Keller he strode over to the pair, side stepping equipment and dodging nurses. Just before he reached them he was spotted by Woolsey who turned and said, without trying to hide his relief.

"Colonel, you're back. I'm glad to see you."

"Sorry it took so long, we had no idea what was happening."

"We didn't know until they were here. The comms array was taken out almost immediately." Woolsey stated.

John looked at the bureaucrat concerned that their normally calm leader was so badly shaken, his face weary, his eyes drowned out by dark circles, his clothes bloodied and torn.

"We're getting reinforcements from the Daedalus, hopefully this mess will be cleared up soon." John said trying to offer hope. "How's Lorne?"

"Stable." Jennifer said turning to face John. Seeing how tired she looked he wondered how she was able to stand. "He's out of the woods, but still faces a long recovery." She paused then added sadly. "I lost Astil. I'm sorry."

"Not your fault doc." John said firmly just as he caught sight of a bruise on her face. "What happened?" He asked. When Jennifer stared at him blankly he reached out and indicated her face. Confused Jennifer raised a hand and touched the swollen area, wincing as she did so. Shrugging she said.

"The Wraith got in here. It's nothing."

Raising his eyebrows he widened his focus to look at both of them and added. "Don't take this the wrong way, but you both look like you need a break."

"That's probably true." Woolsey smiled wryly. "But for now there is too much to do. Besides I'm not sure I'll be sleeping anytime soon."

"And you doc?" John asked.

"Too much to do." Jennifer replied wearily. "I need to be here to run tests when Lorne wakes up."

Knowing he wouldn't be able to change their minds John reluctantly nodded and asked. "Anything you need me to do? If not I'll help with the search."

"The search is the top priority right now." Woolsey said. "After that we need to find out how that signal got turned on and ensure nothing like this happens again."

"Agreed." John replied before adding. "I'll be back later to check on you." Feeling guilty he hadn't prevented the attack and guilty that he hadn't protected them he turned and left the infirmary. Once out he reached for his radio and barked.

"McKay?"

"What?" Was the stressed response from the physicist.

"Give me a sitrep." John ordered.

"Everything's screwed." Rodney said bluntly. "It'll take weeks to put it all back together."

"McKay!" John growled.

"But I will have scanners working within the hour. All going well we should have comms and within twelve hours."

"Work as fast as you can. And find out how the hell we started transmitting." John said before hurrying to find the search teams.


	7. Chapter 7

"Where are we?" Woolsey asked as he entered the briefing room. Not waiting for him to sit John said.

"The city is clear. We're safe, for now anyway."

"That's good to hear. How about the damage?"

"Critical systems are operational, but not at a hundred percent." McKay answered. "Non-critical systems range from operational to screwed beyond belief. Some of them can not be fixed without new supplies from Earth."

"I assume you have filled out a requisition form?"

"Yes."

"I have managed to get the long range sensors working, they're not perfect, but good enough to allow us to track the Wraith."

"And?"

"And, none of the other Hives are moving towards us. The signal that was transmitted was actually relatively low power. My guess is that the other Wraith are too far away to have picked it up."

"Guess?" Milton asked unconvinced.

"Yes guess." McKay replied, not hiding his annoyance. "But right now it's all we got."

"But your educated guess tells you we are safe for now?" John asked.

"Yes."

"Good." Woolsey acknowledged before looking round the table at Jennifer who looked liked she had not had any rest for weeks. Trying not to focus on her dishevelled hair and bruised face he asked.

"How are things in the infirmary?"

"The gym has been cleared. Most were released back to their quarters, those requiring supervision are on the Daedalus. The infirmary is still full of critical patients, but they should all, with time, make a full recovery. We're using six hour shifts to allow enough cover, whilst allowing the team to get some rest."

"Good work." Woolsey smiled encouragingly before John asked.

"Where's Hamilton?"

"In the infirmary sleeping. We had to sedate him." Jennifer said.

"Alright for some." McKay muttered glaring at his still present IOA shadow.

"Where's Ms Muarto?" John asked, noticing Woolsey's shadow was also missing.

"In her quarters. She was one of the walking wounded and has been ordered to rest." Woolsey explained.

"Are you going to get into trouble for losing so many IOA reps?" John questioned, only half in jest.

"I'll find out in a few days. Moving on. Where are we in terms of knowing what happened?" Woolsey asked.

"The signal came from an artefact in Lab 209-kilo." McKay stated, sounding less sure than normal.

"Remind me which one that is?" Woolsey requested to tired to think.

"The one we opened a month ago." Rodney said.

"The one you didn't trust anyone to go in?" Milton asked.

"Yes. The only ones who went in were Zelenka, Milton and I." McKay confirmed, glaring again at Milton.

"So one of you triggered the activation?" John asked.

"That would be a safe bet." Rodney said, almost squirming in his seat.

"How and who?" John questioned.

"I don't know yet." Rodney confessed.

"Because?" Milton probed.

"Because I have not had enough time to investigate."

"Wrong. It is because you don't keep appropriate notes. You have no idea if you even touched that artefact." Milton said smugly.

"This is not the time for finger pointing." Woolsey stepped in. "Right now we need to find out how and make sure it never happens again."

"I disagree." Milton argued. "Poor process at best has hindered the ability to work out what happened and at worse caused the attack. This must be investigated now."

"Dr Milton, last I checked I was in charge of Atlantis." Woolsey shot back. "If Dr McKay is to blame I have no doubt that he will find the evidence and present it to us. If that is the case he will be punished appropriately. However, right now my concern is the safety of this city and its people. Dr McKay does not need to jump through hoops or change his working style to do that."

Milton opened his mouth to speak, but Woolsey shot him a look that put the scientist back in his place. Knowing that he had won the battle for now he looked round the table to ensure no one had anything to add. Seeing the weariness in everyone he knew he needed to wrap things up.

"Okay then. If no one has anything else to add we'll call it a day. Ronon please escort Dr Keller to her quarters and make sure she rests." As Jennifer started to object Woolsey raised his hand to silence her and went on. "Dr Keller, your staff has everything under control. The last thing they need though is you collapsing from exhaustion. If anything happens they'll radio you."

Not waiting for any more arguments Ronon stood and went over to Jennifer, pulling her chair away from the table to encourage her to stand. Wearily Jennifer stood and allowed Ronon to guide her from the room.

Once she had left Woolsey turned back to McKay and said. "Dr McKay I want to know as soon as possible how it happened and I want safe guards in place to stop it happening again."

"Already on it." Rodney assured him.

"In that case I suggest we call it a night." John said taking charge. Looking at Woolsey he said. "Go rest. I've got it."

"Thank you Colonel." Woolsey said gratefully before wearily disappearing from the room.

-00-

"How you doing?" Ronon asked as they walked down the corridor.

"Great." Jennifer mumbled sarcastically, before sighing and saying. "Sorry, I'm just tired and there is still too much to do."

"It'll get done." Ronon said as they entered a transporter. He watched as Jennifer leaned against a wall and shut her eyes. As much as he wanted to say something he couldn't find the words. Eventually he said. "He'll be okay."

"Who?" Jennifer asked sleepily.

"Lorne. He's a fighter, he'll be okay."

"I hope so." Jennifer said, too tired to be confused by the direction of the conversation. Ronon started to say something else only to be interrupted by the doors opening. Noticing Jennifer not moving he said.

"We're here."

"Hmm?" Jennifer asked, her eyes still shut.

"Your stop." Ronon said, unsure if Jennifer was actually awake.

When he did not get an intelligible reply he moved closer to her and lifted her up. Shaking his head when she didn't stir he carefully carried her to her quarters.


	8. Chapter 8

Jennifer awoke confused and disorientated. Her head pounded, but she was sure she hadn't been drinking. Looking round she was surprised to find herself in her quarters, she couldn't remember coming to her quarters and had no idea how she got there. Sitting up, trying to ignore the pounding in her head, she realised she was fully dressed apart from her shoes. Looking round for some water and painkillers she saw her laptop screen flash. Stumbling over she tried to focus on the reminders that were demanding attention.

Jennifer scanned the first page of meeting alerts before reaching for her radio and calling the infirmary.

"Cole here." Was the calm response she eventually received.

"I'm sorry. I think I slept longer than I meant to." Jennifer apologised, her voice hoarse. "Is everything okay?"

"Everything's fine. All patients are awake." Cole reported cheerily.

"That's great." Jennifer said relieved. "I'll be down shortly."

"No need. Everything is under control." Cole assured her. "But if you insist make sure you get something to eat first. I can hear your stomach from here."

"I'll see you soon." Jennifer responded, ignoring Cole's last comment, terminating the connection. Finding her painkillers she downed the pills, wishing her head would stop pounding. As she crossed her room she caught sight of herself in the mirror and groaned before heading to the shower.

Twenty minutes later, feeling more refreshed, Jennifer emerged from her bathroom with every intention of dressing and getting some food. All of the relaxation her shower had given her was quickly removed however when she

Saw her quarters' door opening. Knowing her radio was too far away she reached for the heaviest thing within reach and waited. Her breathing stopped and her heart pounded as the door inched open. She raised the object ready to strike when she heard a familiar voice call.

"Keller. You okay?"

"Sheppard?" Jennifer asked confused as she lowered her make shift weapon.

"Yeah. Sorry to break in, but when you didn't respond I got worried. With your luck I assumed the Wraith were back." John explained, the relief plastered on his face.

"I was in the shower."

"I can see that." John said, causing Jennifer to quickly look down and make sure her towel was still wrapped round her. "Anyway. I'll let you get dressed. I'll wait outside." John added backing away.

As the door shut Jennifer shook her head and tried to find a clean uniform wondering what had brought John to her room.

Having dressed she looked in the mirror and tried to neaten up her appearance as much as possible, but knowing there was nothing she could do quickly to remove the bags under her eyes or the bruises she sighed and stepped out of her quarters.

"How're you feeling?" John asked.

"Okay I guess. I can't believe I slept that long. So what brings you here? Has something happened?"

"No. I'm under orders to make sure you eat."

"Orders? From who?"

"My lips are sealed. I was threatened with pointy needles." John grinned.

"Don't you have better things to do?"

"Actually no. Everything I need to have done has been done. The clean up is being run by McKay's team and he's made it clear that my presence is not helping. So I thought I'd check up on you and make sure you got a decent meal."

"I'm fine." Jennifer assured him.

"That's good. But it doesn't mean I'm not taking you for…" he paused and looked at his watch and saying, "a late lunch. So shall we?"

"Okay." Jennifer agreed, sure there was some ulterior motive.

As they moved through the corridors Jennifer couldn't help but be taken aback by the carnage. Noticing her surprise John said.

"You look like you weren't expecting the city to still be scarred."

"I guess I wasn't. During the attack I was in the infirmary. When it was all over I was rushing between the briefing room, gym and infirmary. I guess I just didn't take in how bad it was." Jennifer explained.

"On the bright side it could have been worse. A lot worse." John smiled before sobering and adding. "It was close. Too close."

"It was." Jennifer agreed. "But we survived." She then paused and added sadly. "Well most of us did."

Not able to think of anything to say John let the conversation stop and they walked silently into the Mess Hall. Unlike the parts of the city she had just seen the Mess Hall looked almost unscathed.

"I might have guessed this would be fixed first." Jennifer smiled.

"An army marches on its stomach." John pointed out as he guided her to a table where Teyla, Ronon, Woolsey and a tray of food were already waiting.

"Hey." Jennifer said as she sat down.

"Jennifer, it is good to see you looking more refreshed." Teyla greeted, still concerned with how tired Jennifer looked.

"Thanks. I can't believe how long I slept."

"You clearly needed the rest." Woolsey smiled, trying to hide his own weariness.

"I guess I did. I can't even remember getting to my quarters." Jennifer said.

"Well technically you didn't." John teased earning himself a kick from Teyla who quickly steered the conversation.

"It is of little surprise, you pushed yourself too hard."

"I didn't have much choice." Jennifer said confused by John's comment, but putting it down to her own tiredness.

"Unfortunately, needs must." Woolsey agreed.

"Has there been any sign of Hamilton?" Jennifer asked, wondering how long she could delay meeting him.

"He's gone." John answered.

"What do you mean gone?"

"The Daedalus left a few hours ago. All the IOA representatives were onboard." Woolsey said.

"That was sudden." Jennifer pointed out.

"We thought the sooner it got back to Earth the sooner reinforcements and supplies could come. The IOA reps were more than happy to go." John explained. "In return we've got a few of the Daedalus crew to keep us going."

"So no more performance reviews?" Jennifer asked happily.

"No. They'll still be submitting their reports." Woolsey explained, noticing Jennifer's face fall he added. "I'm sure you'll have nothing to worry about. You and your team did a remarkable job. Anyway I need to get back to my office. I'll see you all later." He added before leaving.

"Don't look so worried doc." John said, before asking. "Why do you look so worried?"

"Hamilton already had enough complaints to fill a book before the attack. Then during the attack I basically told him to go jump."

"You did? Really?"

"Yes really." Jennifer groaned.

"Good for you." John grinned.

"I'll remind you that you said that when I'm fired." Jennifer said standing. "Anyway I need to get to the infirmary."

-00-

When Jennifer entered the infirmary she was pleased to see it looking almost normal. Scanning the room she walked towards where her staff was loitering and apologised.

"Sorry for taking so long. Is everything okay."

"Not a problem and everything is fine. Don't take this the wrong way but you look like you could do with another break." Cole answered.

"I think that is true for everyone." Jennifer pointed out. "For now I want everyone limited to a maximum six hour shift, preferably four. Which means you're off duty. Get some rest."

"Okay, but I'll be back in six hours." Cole replied before leaving Jennifer to get up to speed. Her first task was to see Lorne who she was pleased to see was awake.

"Hey doc. I thought you were ignoring me." He half smiled.

"Not sure that's possible." Jennifer replied. "How are you feeling? Pain under control."

"They've got me on the good stuff."

"That's good." Jennifer said as she noticed all the cards by his bed. "Did we get a postman in my absence?"

"Turns out I'm the most popular Major in the city." Lorne grinned.

"So I can see." Jennifer said raising an eyebrow. "Where did your admirers even get cards from?"

"No idea." Lorne shrugged, before slurring. "It does show good resourcefulness though. I like that in a woman."

"Okay then. Well I'm going to let you get some rest." Jennifer said turning to leave, only to feel Lorne's hand grab her forearm. As she looked back Lorne said.

"I heard you saved my life. Thanks." Before she could reply the Major had fallen to sleep.


	9. Chapter 9

"Thank you for coming so quickly." Woolsey said as Jennifer took a seat in the crowded briefing room. "I thought you'd all like to hear the news as soon as possible." He paused to ensure that everyone was listening. Content that they were he went on. "Some of you may be aware that Colonel Carter has been working on a programme to develop a new type of ship. One that is to provide defensive capability rather than offensive. The first of this new class, the Ivangorod-"

"Ivangorod?" John asked.

"Yes, named after the medieval fortress in Russia." Woolsey explained.

"So it's a Russian ship?" John probed.

"This is an international project, Colonel." Woolsey said patiently. "But it will be manned with a stronger Russian presence than the Apollo or Daedalus. As I was saying the Ivangorod has been designed as a type of fortress, what it lacks in speed and agility it makes up for with an impressive weapons array and shielding, not to mention size." On seeing McKay's agitation he quickly said. "The full specs will be available to look at later." Pausing to check everyone was still listening he smiled then said. "It has been decided that instead of posting the Ivangorod to here or to Earth, it will become a new Midway station. A stargate has already been installed and twenty minutes ago we received an incoming wormhole from the Ivangorod, which is sitting between us and Earth."

"I thought they scrapped Midway due to the risks." John said, surprised this was the first he had heard about it.

"They did." Woolsey agreed. "But the defensive capability of the Ivangorod is such that a repeat situation is unlikely. Also the Ivangorod will not be in a fixed position. To travel to Earth you would gate to the Ivangorod then the Ivangorod would travel for three days towards Earth. You would then gate from the Ivangorod to Earth. It will not be possible to travel from here to Earth without the three day transit time."

"That's the only reason?" John asked dubiously.

"Officially yes." Woolsey stated as he removed his glasses and cleaned them. Having placed them back on he leaned forward and said. "Off the record, the distrust between various governments meant that no one wanted it sitting above Earth. By using it to house a new midway gate it places it in an important strategic position that no one can object to, but is out of the way. But regardless of the reasons this is good for us. Although it is not fully operational yet, within the next month we will start receiving regular supplies and extra personnel through it."

"That kind of assumes they'll give us extra resources." John said.

"I know. But we gave the IOA representatives a somewhat biased experience on life here. I can only hope some good comes from that and they fight our corner. At the very least personal mail can once again be passed between here and Earth on faster timescales, which will help morale."

"True." John said.

"It also means it's easier for the IOA to interfere." Rodney pointed out as typed at his laptop only half paying attention to the meeting.

Ignoring the comment Woolsey said. "We have been asked to assist the Ivangorod by testing the link, through sending personnel back and forth."

"We're already down on numbers." John said.

"I know. But the Ivangorod has a fully equipped infirmary. As it will be leaving for Earth tomorrow I thought we might want to make use of the facilities currently available to us, we could borrow some of their supplies."

"Doc?" John asked, unconvinced.

"The infirmary is still near capacity, if we could move and treat the less severe on the Ivangorod it would be a help." Jennifer replied.

"Excellent, I will contact the Ivangorod and let them know. I'll also find out if they have any spare resources we could have." Woolsey said standing. "I'll let you know what they say."

As he left the room Teyla looked at John asked.

"Problem?"

"Don't know. Something just doesn't seem right. Why weren't we told about the plans before it was posted at Midway?" John said, clearly bothered.

"It was probably never meant to be a Midway." McKay said as he typed away at his laptop. "You heard Woolsey, it is only being posted here as no one trusts anyone else to have one in orbit around the Earth.

"I can't believe that is the only reason, there must be something else. Something sinister for us not to get told." John replied.

"Can't we use the personnel transfers as a way of investigating the reasons?" Teyla asked.

"We can, but we'll have to be careful. If it is on the level we don't want to cause a diplomatic incident." John agreed just as McKay exclaimed.

"I knew it! It was that self serving arrogant-"

"What is it Rodney?" John interrupted.

"Look at this." The physicist said thrusting his laptop at John.

"What am I looking at?" John asked, recognising logs and a graph but not what they represented.

"On the left are the entry logs for the lab. On the right is our RF signature."

"Our?" John asked.

"The city. I've managed to extract sensor information and reconstruct our RF profile. You can see that normally we emit low level radiation, occasionally we communicate to the Daedalus or Apollo and you get a small spike." He explained pointing to the graph.

"So the big spike is where we sent the Wraith the 'We're here. Come and eat us' message?" John guessed.

"That's right. On the left are the security logs for the lab."

"Okay." John said not seeing what McKay was getting at.

"Five minutes before the transmission started someone enters and shortly after it starts to transmit they leave. Coincidence? I don't think so."

"Let me guess, that person is Milton." John said.

"Got it in one."

"You think he activated the beacon deliberately?" Teyla asked. "To what end?"

"Who knows? It could just as easily be incompetence."

"Kinda an important distinction." John pointed out. "Was there anything he could have gained from deliberately setting up the transmission?"

"The destruction of Atlantis?" McKay guessed. "I mean he left with us minutes after that transmission started. He was effectively safe."

"You think it was the Trust again?" Jennifer asked.

"Last time they had a full game plan. This time I can't see what their end game is." John replied.

"Doesn't mean there isn't one." Ronon shrugged.

"Why was he in the lab?" Jennifer asked. "Shouldn't he have been prepping for the mission?"

"No idea, he shouldn't have been in there."

"Okay, I'll report this to Woolsey and work out the best way to get the info back to the SGC and Daedalus." John said. "In the mean time, Rodney, work out what could be gained from setting the beacon and how easy it is to do accidently. Everyone else, look for any changes or anything different that could have been done during the attack."

"You think he wasn't working alone?" Jennifer asked.

"If he really is an operative, we have to assume he had backup. The other IOA reps are obvious choices but it could be anyone." John said. "Until I know for a fact it wasn't incompetence we keep searching."


	10. Chapter 10

"Hey." Rodney greeted as he met Jennifer in a corridor.

"Hey." Jennifer replied as she kept on walking.

"Where are you going in such a hurry?"

"Woolsey wants to see me." Jennifer explained.

"Really? That's strange." Rodney commented. "He wants to see me as well."

"About what?"

"No idea, he just asked me to come up as soon as I could."

"Me too." Jennifer said, starting to get concerned. "Should we be worried?"

"Not sure." McKay responded before they silently made their way to Woolsey's office. When they entered and saw that no one else had been summoned neither could work out if it was a good or bad thing.

"Please sit." Woolsey said as he looked up from his computer. "As you know the Ivangorod has just returned to within gate range of us. I have received a communication from the SGC relayed via the Ivangorod. Firstly, you'll be pleased to know that the Daedalus is now within comms range of Earth and all our injured have all survived the journey and are doing well."

"That's nice, but not the reason we're here." Rodney pointed out.

"True." Woolsey said, pausing to removed his glasses and clean them. Once they were back on his nose he was about to continue, only for McKay to ask.

"Is this about Milton? Have they discovered he is a Trust operative?"

"No, this is not about Milton's possible involvement with the Trust. The information you uncovered has been passed onto the relevant parties and an investigation is being launched, by both the SGC and the IOA."

"Then why am I here?" Rodney asked, causing Woolsey to lean forward and say.

"It turns out the IOA representatives have used their time onboard to complete their reports. These have subsequently been submitted to the IOA. As a result of the reports they have requested that both of you return to Earth, via the Ivangorod, for a debriefing."

"We're being removed from post?" Jennifer asked, jumping to conclusions.

"I don't believe so." Woolsey said carefully. "It was always the IOAs intention to personally debrief a small number of the heads of departments. You could have been selected at random."

"And there's a pig flying past the window." Rodney shot back. "Face it we're being recalled as we've been deemed to have failed a stupid test they set. What I don't get is why I'm being sent for. I proved that Milton was incompetent. Isn't the timing a little suspicious as well? I mean first the IOA visit, during which time Milton instigates a Wraith attack, then the whole Ivangorod becoming a Midway overnight when none of us were consulted, now I'm getting recalled, something doesn't sit right."

"Dr McKay, firstly performance reviews happen every six months; secondly as far as I understand it all of the investigations that Colonel Sheppard isn't running and of which I have no knowledge have returned nothing, implying that the Ivangorod is not part of some evil scheme; finally both you and Dr Keller have been recalled."

"That is a flaw I'll grant you, I mean take me away and the city could fall, but Jennifer well people may get sick, but the city will stand." McKay said, earning a chastising shake of Woolsey's head. "There has to be something more to it."

"All I know is that you have been requested and you are to be prepared to transfer to the Ivangorod in twenty hours." Woolsey said.

-00-

"Doc." John said as he hovered in Jennifer's doorway.

"Something wrong?" Jennifer asked looking for signs of injury.

"No, I just came to see you."

"You've heard then?" Jennifer guessed as she turned and resumed packing.

"Anyone within a mile of Rodney has heard." John explained. "Woolsey could be right, you could have been picked at random."

"You believe that as much as I do."

"Look doc, I just want you to know and believe that you are a great CMO and your place is here. Don't let anyone tell you differently."

"Thanks." Jennifer said, touched but unconvinced.

"You'll be back here in no time." John went on.

"Uh huh."

"Seriously doc, you'll be back soon. There's really no need to pack for a year long trip." He pointed out nodding to the bags on Jennifer's bed.

"I'm not taking all of them." Jennifer assured him.

"So why does it look like you're going to pack them?"

"I said I wasn't taking them, not that I wasn't packing them."

"Why are you packing bags you're not taking?"

"In case I don't come back. This way everything is ready to be shipped." Seeing John pull a face she added. "The thought of someone going through my stuff kinda freaks me out."

"Please tell me you don't do this before every mission."

"Of course not. If I don't return from a mission I'll probably be dead so wouldn't care who went through my stuff."

"Right." John said, wondering if he should be concerned that Jennifer had given it so much thought. "Anyway we're having a movie night tonight, you should come."

"Thanks, but-" Jennifer started only for John to cut in.

"By 'you should' I really meant 'you will'. If you're not at my quarters by eight I'll send Ronon to find you."

"Fine I'll be there." Jennifer agreed.

"Good." John grinned, happy he had done his job.

-00-

By the time it got to just before eight Jennifer was feeling tired and depressed. Having packed her bags she had spent the next few hours going through different possibilities of what awaited her on Earth, none of them had a happy ending. She was feeling miserable she was tempted not to go to movie night, but the thought of Ronon having to collect her forced her into going. Sighing she had another look round her room, convincing herself she had packed everything she should before walking over to John's quarters.

As she walked down the corridors she walked past an empty balcony and found herself drawn to the view. She stood in the breeze staring out at the water as it lapped round the base of Atlantis. She remained lost in thought until a familiar voice said.

"Doc."

"What are you doing here?" Jennifer asked turning. "You should be in bed. That's what bed rest means."

"I know what bed rest means." Lorne said. "But I needed to get over to the Colonel's quarters and this corridor is the quickest route. The only reason I'm not sitting down right now is I saw you and had to redirect you before the everyone finds out you got lost."

"I did not get lost. I just wanted a final look at the view."

"None of that." Lorne said, stiffly walking over to Jennifer. "You'll be back. Either because you're on the next flight back or because we'll come and get you."

"Not until you're fully healed." Jennifer warned.

"I promise." Lorne said before hugging Jennifer and assuring her. "It'll be fine." Pulling back, trying to hide a wince of pain Lorne said. "We better go or Sheppard will send a search party."


	11. Chapter 11

"How can they keep him for so long?" Jennifer asked, pacing by Sam's desk.

"Probably because he is arguing every point." Sam replied.

"But he didn't do anything wrong, he proved it was Milton."

"But if Milton activated it by accident Rodney will still be held accountable." Sam explained.

"So we have to hope Milton is working for the Trust and was trying to destroy Atlantis?" Jennifer asked.

"I wouldn't go that far. Look, Rodney has a skill at rubbing people up the wrong way. A lot of them will view this as pay back. These meetings are just to show everyone that the IOA is in charge." Sam tried to assure her friend as her office door opened so fast she thought it would come off the hinges.

"How'd it go?" Jennifer asked nervously as Rodney stormed into Sam's office.

"How do you think it went? It was a disaster. Their sole purpose was to make themselves feel big. The only way it could have been worse was to have Ellis on the panel. Milton nearly destroys Atlantis and they blame me for not employing proper processes, they don't even question or punish Milton. They're after blood. They're worse than the Wraith. I'm just glad it's over. I can't think of anything worse th-"

"Rodney!" Sam cut in, trying to stop the physicist undoing all the calming work Sam had implemented over the last three hours.

"What?" He snapped. Seeing her nod towards a very pale Jennifer he said. "But I'm sure you'll be fine." Turning his attention back to Sam he said. "You realise this is all your fault. If you hadn't built the Ivangorod so quickly, I wouldn't be here now."

Before anyone else could speak the door creaked open and Landry entered saying.

"Dr Keller, they're ready."

Nervously Jennifer stood and walked to the door barely acknowledging the good luck she got from Sam. As she walked the corridors of the SGC next to Landry, the General suggested.

"Try not to look so nervous. What's the worse that could happen?"

"I'm removed from my post." Jennifer said immediately.

"I seem to remember not so long ago you tried to remove yourself from your post." Landry pointed out.

"That seems a long time ago." Jennifer confessed.

"What changed?"

"Back then I ended up with the job due to Carson's death. I never even thought about being CMO until I was given the role. I could see the doubts in others over my lack of experience and I doubted myself. But now I know I can do a good job. I have done a good job. I don't want to give it."

"You don't need to convince me." Landry smiled. "I'm behind you one hundred percent. Just take that attitude in with you and you'll be fine."

Taking a deep breath Jennifer walked into the conference room to face the lions. The first thing that struck her was how many people were in the room. She had assumed there would be three or four IOA representatives, instead there were twelve, including Hamilton. Also seated at the table was General O'Neill.

Picking up on Jennifer's surprise at seeing him, the General stood and walked over to her. "Good seeing you again Dr Keller." He greeted shaking her hand. "Please take a seat next to me." As Jennifer walked over to the chair he added. "You're probably wondering why I'm here, seeing how you are not military and the fact I hate IOA meetings. The answer is you are responsible for the well being of my people so I have a vested interest in the proceedings." As Jennifer sat he leaned closer to her and whispered. "You'll be fine. I'm on your side."

When Jennifer was settled a man she didn't know looked at Jennifer and said.

"I'm Patrick Garton. I am currently the chair of the IOA. As such I am in control of these proceedings. I am aware that there were some extreme events that took place during Dr Hamilton's visit."

"That's a euphemism if ever I heard one." Jack muttered. Ignoring him Garton went on. "It was not my intention for you, or the others, to be assessed under such conditions. However, I have asked all the subject matter experts to include events that happened in their reports so we could get a rounder picture of what your role is like." He paused before passing Jennifer a very thick file.

"How many trees did that cost you?" Jack asked commenting on the size.

"That," Garton started, ignoring the General again, "Is the detailed report that Dr Hamilton prepared. I would like to thank him for being so thorough. In the interest of time I suggest that we do not go through the report now, instead we will go through the key points now and you may refer to the report at a later time. Dr Hamilton please begin." Garton finished as Jennifer's heart sunk.

"Thank you." Hamilton said. "As you are aware I was sent to appraise Dr Keller in her role as a doctor and as CMO of Atlantis. Like many of you I went with several concerns such as her lack of experience, the lack of a formal interview process she went through to get the role of CMO and the number of resources she was asking for. As such I was not only asked to appraise her, but to see if she was in fact the right person for the job, either now or at some point in the future." He paused whilst he took a sip of water. "During my first few days my concerns were realised. Dr Keller set up off world clinics in an almost haphazard way. She spent too much time pandering to the locals. As such a mission that should have taken two hours took eight."

"Hang on a minute-" Jack jumped in only for Garton to raise his hand and say.

"General please let Dr Hamilton finish. Dr Keller will have a chance to respond when Dr Hamilton is done. Until then please keep silent." Reluctantly Jack bit his tongue all the while glaring at Hamilton, who continued.

"Back on Atlantis things were not much better, the infirmary had a very relaxed command structure with no obvious chain of command. All of the staff, but Dr Keller especially, were not detached enough from the patients. Dr Keller spent too much time with the patients rather than her research. All in all after two days I was of the firm belief that Dr Keller should either not continue in her role, or only continue if a stringent framework was set up to allow her to appreciate her duties more." He paused again and sipped his water. "As you all know I have a strong background in emergency medicine and the practice of medicine in extreme environments. I therefore assumed I was an ideal person to mentor Dr Keller through all changes that needed to be made."

Hamilton then looked directly at Jennifer who had lost all hope. He then gave a half smile and said. "One of the great things of experience is to be able to be critical of others, in order to improve their performance based on your knowledge. One thing that does not become easier with experience is admitting you were wrong. Yet, that is exactly what I am about to do. During my time there the Wraith attacked. At that point the whole city turned into a warzone. Dr Keller split her staff in two. One half stayed in the infirmary, the other set up a triage clinic in the gym. She did not send her most experienced doctor to run the triage centre as I would have done, instead she kept the best with her to tend the critically injured who were coming in. The staff knew what equipment and supplies to take, without instruction, showing that they are well drilled and all equally important cogs in the machine. She worked for hours without rest in surgery, something that should normally be frowned upon, but on Atlantis is a necessity due to the lack of staff. She showed great resilience and flexibility saving me from a Wraith one moment and going back into surgery the next. Although her leadership style is informal she is fully capable of setting boundaries when needed and has done so to produce a well run infirmary."

He stopped again for a drink before finally saying. "To conclude then, it is true that I would not run the Atlantis Infirmary as Dr Keller does. But that is not to say that Dr Keller's method is incorrect. We both come from different view points and I believe we could learn a lot from each other. Whilst I would like Dr Keller to take on board some of the suggestions I make in the report, that should not be mandated. In fact the only action I would insist on is for this board to review the budget and give Dr Keller the resources she requires to do her job."

"Thank you Dr Hamilton." Garton said before looking at Jack. "General I believe you wanted to disagree with the doctor."

"Only the first half. He rescued it later on." Jack shrugged.

"Good. Dr Keller do you have anything you want to say?"

"No." Jennifer said shocked and confused by what had just happened.

"Very well." Garton said. "I'm guessing you would like to make the Daedalus flight back to Atlantis, which departs in four hours." He waited for Jennifer to nod before going on. "In which case I'll give you the highlights of our recommendations. We have agreed that you can have two more doctors and three nurses. Recommended personnel files have already been sent to you. I suggest you review them on your flight back and once you have picked let us know. " Standing he turned his focus to the rest of the room and said. "I believe we are done here. Thank you for your time." With that he left, quickly followed by the rest of the IOA.

As Jennifer continued to sit there in a state of shock and confusion Jack nudged her and said. "You know you can leave now?"

"That's it? I'm not fired?"

"No. Unless they're speaking in some sort of reverse code, but I'm pretty sure they're not." Jack said standing. "Come on, let's get you back to Carter's office where I'm pretty sure there is a hidden supply of real coffee."


	12. Chapter 12

Jennifer sat in the darkened mess hall on the Daedalus scanning the latest lab results from Atlantis, frustrated she was still two weeks away from her home. Reaching over to her coffee she took a sip and pulled a face when she realised it was cold. Surprised she looked at her watch and shook her head when she realised she had been there for over an hour. She thought about getting herself a fresh cup, but knew if she did that there would be no chance of sleep. Instead she pushed the mug to one side and went back to the lab results and reports.

She was so engrossed in what was on her screen she didn't notice another person enter the mess hall. Nor did she notice when the other person stopped, looked round and then crept forward towards her. She remained oblivious to their presence until she felt two hands on her shoulders, close to her neck.

Spinning round, unable to stop a small scream escaping Jennifer's expression turned from fear to relief to annoyance in under a second.

"Laura! Are you trying to kill me?" Jennifer asked.

"Just startle you. I'd say I did a pretty good job." The marine grinned.

"What are you even doing here? I thought you were on a SG team."

"I was. After your recent exploits they decided to increase the marine presence on Atlantis, so I'm being redeployed."

"You're staying on Atlantis?" Jennifer asked happily.

"I am." Laura grinned. "But enough about me I want to hear the truth about what's been happening with you. I've been hearing all type of crazy rumours about you."

"Like what?" Jennifer asked looking worried.

"That you've, personally, been fighting the Wraith. You told someone from the IOA to go jump. You fought to stay on Atlantis. Need I go on? So is this new found assertiveness you or have you been taken over by some sort of Pegasus parasite."

"Not that I know of." Jennifer replied.

"In which case how did you manage to fight off a Wraith? I mean no offence, but last time I saw you, you couldn't even fight off that butterfly on P27."

"That was not a butterfly, it was an evolved monster that happened to resemble a butterfly." Jennifer said firmly.

"It was a butterfly." Laura responded. "So when and how did you learn to fight?"

"Ronon taught me." Jennifer said, immediately wishing she hadn't when Laura broke out into a huge grin.

"He did did he? And were they private lessons?"

"Yes."

"You two alone in a gym, getting hot and sweaty?" Laura questioned, the smirk cemented in place.

"Do you have a point?"

"I can't believe you didn't tell me you and Ronon were together. You should have opened with that."

"We're not." Jennifer said.

"Why not? For him to give you private lessons he's clearly interested. Perhaps you need to give him a push."

"I did. The other way."

"What do you mean?" Laura asked confused.

"I told him I was interested in someone else."

"You did?" Laura questioned, looking surprised. "Who is it?"

"No one."

"No one? You lied? Why?"

"It's complicated."

"I'd expect no less from you." Cadman said. "Tell me all."

"Not much to tell, I got confused and scared and panicked."

"Ronon, the big muscular man who women throw themselves at, shows interest in you. How is that confusing?"

"It wasn't that that was confusing me. It was Rodney."

"Rodney? As in Rodney McKay? What has he got to do with this?"

"A while ago he got infected with a parasite, which changed him. I saw this whole other side of him, he was sweet and sensitive. And he recorded a video where he said he'd fallen in love with me."

"He did what?" Cadman asked. "Rodney McKay told you that he loved you?"

"Keep your voice down." Jennifer pleaded as she looked round the mess hall, checking it was still empty. "He didn't tell me in person, he recorded a video of which he has no recollection."

"So you fell for a Rodney that you'll only ever see again if you infect him with a parasite, who has no recollection of saying how he felt?" Laura summarised.

"Yes. No. Not exactly. I thought I might be falling for him, or the idea of us. I mean we're not all that different."

"Compared say to you and Ronon?" Laura guessed.

"Yes. I mean we're so different. I didn't think we'd stand a chance. And I didn't want to start something if I may have had feelings for Rodney."

"Fair enough, but you and Rodney you're not dating are you?"

"No. Rodney is back to being absorbed in his work. I doubt he'd be interested in a relationship."

"I'm sorry." Laura replied.

"I'm not. I'm still friends with Rodney, nothing has changed and I'm happy with that. Ronon on the other hand is a different story. I think I really hurt him when I said I was interested in someone else. Since then he's been distant and we have barely spoken. I really miss what we had." Jennifer said sadly.

"You could talk to Ronon." Laura suggested.

"You're suggesting that I have a heart to heart with Ronon?" Jennifer asked raising her eyebrow.

"Phrased like that, the idea needs work." Laura confessed. "Fortunately we've got a long trip to figure it out."

"Or we could just forget it." Jennifer suggested.

"Not a chance." Laura replied. "The big question is do you want what you had or do you want more?"


	13. Chapter 13

"Morning Rodney." Jennifer greeted as she sat opposite him.

"Morning." He said distractedly, without looking up from his screen.

"That's not very polite." Cadman pointed out as she sat next to Jennifer. On hearing Laura's voice Rodney's head shot up and groaning he asked.

"What are you doing here?"

"About to have breakfast." Laura smiled.

"I meant why are you here, on the Daedalus?"

"Well it's a long walk to Pegasus."

"You're being posted to Atlantis?" Rodney asked, his face falling.

"I always like the way you make me feel special." Laura shot back sarcastically.

"That's your fault for what you did to my body."

"You make it sound like I tortured you. I just took your body to the gym and for a run. You should thank me. I halted the development of breasts. Men shouldn't have breasts."

"I do not have breasts." Rodney snapped.

"Rodney I saw you naked, as if it were me." Laura pointed out. "As much as I'd like to forget the experience I don't think the SGC will cover the shrink costs I need."

"How about we never discuss it again." Rodney suggested.

"Tempting, but it's best to discuss our issues."

"Funny." Rodney said before something caught his eye. "What are you wearing?"

"My uniform." Laura answered confused by the question.

"Don't think so. Wrong rank." Rodney replied nodding at the Captain's Insignia.

"You got promoted?" Jennifer asked.

"No need to sound quite so surprised."

"I'm not. It's just that you didn't mention it." Jennifer replied. "That's great news. Congratulations"

"Thank you." Cadman smiled.

"When did it happen?"

"Came with the transfer."

"So you get promoted, Jennifer gets praised by the IOA and gets extra resources, whilst I get roasted. How is that fair?"

"Still sore about the Rodney battering the IOA gave you?" Laura asked. "I heard all about it. Sounds like they were pretty rough on you."

"You heard? Has everyone heard?"

"Probably."

"Great, just great."

"You come out the hero." Laura offered.

"I do?" Rodney asked.

"Sure, you took on the IOA, you proved one of them attempted to destroy Atlantis, all that earns you points. What I don't get is why the IOA are not taking it more seriously."

"Neither the IOA or the SGC could find any evidence linking Milton to the Trust." Jennifer explained.

"Still seems sus." Laura commented.

"Either they are all in on it or he has friends in high places." Rodney said. "But if he is involved with the Trust I'm going to find the evidence."

Before anyone could respond Laura suddenly tensed and said.

"Sir."

"Captain, doctors." Caldwell greeted, standing behind McKay.

"Do you want to join us?" Jennifer offered.

"Thank you, but no, I've got a briefing to give. What I would like is for you to come to my quarters in an hour, we need to discuss something."

"Of course." Jennifer replied, wondering what else was about to go wrong.

"Good." Caldwell acknowledged before looking at McKay and saying. "And Dr McKay, whilst you are a guess on board I'd appreciate it if you didn't attempt to blow up my ship." With that he turned and left leaving a fuming Rodney in his wake.

"What is that meant to mean? Is this pick on Rodney year?-"

"Relax Rodney." Laura said. "I think he was joking."

"Colonel Caldwell? Joke?"

"Unheard of I know, but he had an amused twinkle." Laura explained.

"Everyone has lost their minds." Rodney exclaimed standing and heading off to a lab.

-00-

"Dr Keller, thank you for coming. Please take a seat."

"Something wrong?" Jennifer asked, unsure why she had been summoned to Caldwell's quarters.

"I believe so." Caldwell said leaning back on his chair, his arms folded. "During my last visit to Pegasus, whilst you were fending off the Wraith, some of your colleagues expressed concern over the way you were pushing yourself and the hours you were pulling."

"They expressed this to you?" Jennifer asked, feeling betrayed and angry.

"No. I'm not one of the inner circle." Caldwell smiled wryly. "I just overheard the conversation. The point is your friends are concerned about you and aren't sure how to help. I know if I were to ask you about your workload you would have a completely logical reason for all the hours you pulled and an explanation for why no one else could help. All you say could be fact or mere excuses. In the end it doesn't matter. You keep driving yourself this hard you'll go over the edge. I've seen it happen too many times before. Everything is fine right up until its not. Don't let that happen to you." He paused and gauged Jennifer's reaction before continuing.

"I've seen you grow both as a person and a doctor since you joined Atlantis. But there is still a skill you haven't learned. That's how to say 'no'. Until you do the workload will continue to increase as will the pressure." He unfolded his arms and leaned forward. "I don't want to preach at you, I'm just trying to get a point across." He paused and looked like he was about to say something else when his radio interrupted him.

"Go ahead Marks." Caldwell said. There was a pause whilst a frown crossed his forehead until he said. "I'll be right there."

"I'm sorry I have to get to the bridge." He said looking at Jennifer who asked.

"Is there a problem?"

"Don't know. An encrypted message has come in from the SGC. My money is it's not them wishing us a good journey." Nodding Jennifer headed for the door as Caldwell added. "Doctor, if you ever need to talk, my door is open."


	14. Chapter 14

"Doctor." Caldwell greeted as he entered the infirmary. "Thanks for getting here so quickly, especially after I lectured you about working too hard."

"Not a problem." Jennifer assured him. "What's up?"

"We just received this from the SGC, I think you need to see it."

Puzzled Jennifer took the tablet from Caldwell and read the message. Frowning Jennifer looked up and asked. "Where is crewman Davis now?"

"On his way here. Cadman is keeping an eye on him."

"You think he knows?"

"No idea, he could just be a pawn. Best to be careful though." Caldwell said as the crewman entered the infirmary.

"Is there a problem Sir?" Davis asked, looking confused.

"Maybe. Come in and take a seat." Caldwell ordered. "We received a communication from the SGC with the results of the blood tests you had done."

"Is something wrong with me?" He asked looking worried.

"There were some anomalies." Jennifer said. "I'm going to take another sample and run some more tests."

As she drew the blood she asked. "You had a test done at the SGC because you were feeling unwell?"

"That's right ma'am. I felt like I was coming down with the flu. I went and saw the docs who did some tests and told me to rest."

"And how are you feeling now?"

"Worried ma'am." Davis said nervously.

"Before you were called down here, how were you feeling?"

"Fine ma'am."

"Any symptoms at all?"

"No ma'am. I felt better that I had done in a long time."

"That's good. I'm going to need you to stay here whilst we wait for the results."

"How long will that be? They took days to come in from the SGC?"

"The test doesn't take long to run." She assured him. "I should have the results in a few hours. Until then try and get some rest." Leaving him under Laura's watchful eye she headed to the back of the infirmary, Caldwell following close behind. When she was happy Davis would not hear she looked at Caldwell and reiterated.

"It will take a few hours to run the tests."

"As soon as you have the results I want to know." The Colonel said.

"You'll be the first I tell." She assured him before settling down to run the test.

-00-

"Well?" Caldwell asked a few hours later.

"Almost no sign." Jennifer replied. "If I hadn't known I was looking for it I probably would have overlooked it. If you go down to the correct concentration levels the nanites are still there, but they are decaying. In two days time they would have disappeared from his system completely and their existence would become undetectable."

"But he does have them?"

"Absolutely."

"What were they doing?" Caldwell asked.

"No idea, all of his other results from the SGC look normal. I need to do a complete set of tests on him so I can compare the results now to then."

"And in two days time, if they do leave his system completely, is he really free from them?"

"Based on previous experience yet, but we still have no idea who is behind this or what the nanites are programmed to do. Giving Rodney a sample may shed some light on the purpose, but not to the route of infection."

"Is there something else?" Caldwell asked, noticing Jennifer's frown.

"You realise this was caught by luck? His blood only had that test run at the SGC because someone mislabelled the sample."

"What's your point?"

"If Davis really has no idea about this anyone of us could have been infected." Jennifer explained. "I'm hoping that the flu like symptoms he displayed were a reaction to the nanites in his system. If that is the case only those who have displayed cold of flu like symptoms are at risk, mind you that's still a large number of people. But that's a big if."

"Recommendations?"

"Take samples from the entire crew and run tests." Jennifer said.

"Understood. My concern is that we're not meant to know about this and if we start taking samples from everyone it may give the game away." Caldwell said. "I need you to come up with a good reason to take these samples."

"We'll just call it a super flu." Jennifer shrugged. "Enough people on board are coughing that'll seem plausible. I suggest I take samples from the senior crew first, as well as Rodney and myself. I'll show Rodney what to look for so he can independently verify my test results. After that I'll work my way through the rest of the crew."

Rolling up his sleeve Caldwell asked. "Shall we start then?"

-00-

Jennifer looked at the latest test results once more, again finding no traces of nanites. She was please no one else yet had been infected, but she was growing frustrated at not knowing what the cause in Davis was. Reading over Rodney's preliminary report she felt the answer was close, but no matter how she looked at the data it just wouldn't make sense. Putting her tablet down she sighed before standing and stretching. Glancing at her watch she saw it was past two in the morning. "So much for taking it easy." She muttered. Deciding to call it a night she walked back to her quarters, nodding to the very few crew members she passed on the way. When she reached her quarters she flopped down on her bed and closed her eyes only for her mind to start racing as her brain processed all the data that she had seen. She sensed that something wasn't right and not knowing what was frustrating. Knowing sleep wouldn't happen whilst her mind was racing she stood and changed into running gear, hoping a jog would tire her out.

As she started jogging though the decks she found her mind go back to the last time she had taken that route. Back then she had jogged along side Ronon doing her best to keep up. Sighing at the thought of what might have been she tried to concentrate on nanites. Lost in thought she took a wrong turn and ended up in the air recycling room, surprising the occupant.

"Sorry, must have taken a wrong turn." Jennifer panted. Pausing to catch her breath she commented. "You're up late, well early." She had barely finished the sentence when the occupant turned and struck her on the head with a wrench.


	15. Chapter 15

"It's no good, she's not showing up on any scans." McKay said.

"How is that possible?" Caldwell asked.

"Either, she is in some sort of black spot, or she is no longer on the ship or she is … well dead."

"Marks." Caldwell barked. "Have we stopped and let anyone off the ship?"

"No Sir."

"Is there anyway Dr Keller could have left the ship without us knowing?"

"No Sir. I have checked every log. No external doors have been opened."

"Cadman."

"Sir!"

"Are you one hundred percent positive that Davis did not leave the infirmary?"

"Yes Sir." Cadman assured him causing Caldwell to order.

"I want a deck by deck search. I want her found."

"Yes Sir." Cadman agreed before organising her men.

"McKay do what you can with our internal scanners."

"On it." Rodney replied before Caldwell sat back down, wondering how he was going to explain that he had lost the doctor. However, as concerned as he was for Jennifer he was worried that something bigger was going on and in light of the nanite find her disappearance was not a coincidence. Turning to Marks the Colonel ordered.

"Patch me through to Atlantis."

"Go ahead Colonel." Woolsey said after a few moments.

"We have a problem."

"Which is?"

"Dr Keller is missing."

"What do you mean missing?" Woolsey asked. "You are on a sealed ship. How can she disappear?"

"That's what we're trying to work out." Caldwell said, clearly not in the best of moods. "Dr McKay has requested some equipment be sent up here ASAP to help with the search. We'll be in orbit above P29-786 shortly. I'd appreciate it if you could gate the equipment there and we'll beam it up when we arrive."

"Of course." Woolsey agreed, confused and concerned that Jennifer was missing.

"You want anymore manpower?" Sheppard offered.

"It can't hurt." Caldwell said, there was a pause before he went on. "I'm sending you an encrypted file. I suggest you read it before you gate through."

"We've received the file." Woolsey assured him as the bureaucrat and Sheppard exchanged confused glances.

-00-

When the Daedalus finally arrived in orbit John, Teyla and Ronon transported with the first batch of equipment that McKay had asked for. Once on board John immediately headed to the briefing room to find out what was going on.

"Sir." He greeted from the doorway.

"Colonel. Come in. McKay's just about to give us an update."

"I have been through every room in this ship scanning for her. So far nothing."

"You sure she is still on board?" John asked.

"Been through that loop." McKay said. "And it seems like a safe bet. The problem we have is several small sections of this ship turn out to be shielded from the sensors."

"How? Who's done it?"

"No one. It is like that naturally, well kind of. The equipment we use all transmit in RF. There are parts of the ship where these transmissions act to block sensors. It is only low level so the areas are small, but should be big enough to hide a person."

"You know where these black spots are?"

"Yes. The problem is there are at least sixty of them and none of them are easy to get to. The equipment you have brought up may allow me to get through the interference and detect her. Otherwise we'll have to continue manually searching each of these areas. So far we've only covered five."

"How long has she been missing?" John asked.

"Somewhere between eighteen and twenty-six hours." Caldwell replied.

"She still the only one?"

"Yes."

John was about to say something else when McKay exclaimed. "Got something!"

"What kind of something?" John asked.

"Don't know yet, but it is worth checking. The air recycling room. Deck 2 section 23." Rodney said furiously typing away.

Without saying a word John, Ronon and Teyla ran off.

-00-

Having finally reached the air recycling room the trio were disappointed not to see anything out of the usual. As Ronon and Teyla called for Jennifer John radioed Rodney saying.

"Okay Rodney, we're here, where should we be looking."

"Caldwell here. There should be a ventilation hatch on the left hand wall six feet from the entrance."

After a pause John said. "Found it."

"Remove the hatch and there should be a small shaft."

"See it." John confirmed.

"The black out zone is a small area fifteen feet down the shaft on the right."

"Any other way in?" John questioned.

"Negative. Why?"

"It's a tight squeeze, not sure I'll fit." John explained as Ronon called growled.

"Blood."

"Where?" John asked.

"Down here. Someone did a bad job washing it." Ronon said pointing to the floor.

"There's more in the shaft." Teyla said shining light into the darkened tunnel.

"What's going on down there Sheppard?" Caldwell demanded, frustrated at only hearing parts of the conversation.

"Looks like this could be it." John explained. "There are traces of blood here. Teyla's the only one with a chance of fitting down the shaft. It'll take a couple of minutes to remove her tac gear though." John explained.

"I'll go Sir." Cadman said as she ran into the room explaining. "All I need do is remove my jacket."

"Okay." John agreed. "Be careful we don't know what's down there."

Nodding Cadman striped off her jacket and entered the shaft, which even for her was a tight squeeze. Crawling through the narrow space she was concerned with the amount of dry blood she saw. As she reached the fifteen feet mark she saw a loosened panel on her right. Stopping next to it she gripped the edges and pulled it free, revealing an opening to a slightly bigger space. Pulling herself forward her heart sunk when she saw what was occupying the space.

"Jennifer." She called as she tried to squeeze into the space. As she moved closer she was relieved to hear a small whimper come from her friend. Due to the tightness of the room she couldn't get very far, but she did manage to find Jennifer's bound hands and give them a squeeze. "It's okay." Laura assured Jennifer as tried to see if she could cut the ropes. However, due to the tightness of the space there was too much danger of cutting Jennifer.

"Cadman report." John ordered, growing impatient in the recirculation room.

"I've found her Sir. She's alive. It is going to be hard to get her out of here, there's no room to move and she's bound."

"Any plans?"

"Give me a minute." She replied looking round the space.

"I could try a small detonation to increase the opening." She said aloud, but meant for herself. The comment caused a more panicked whimper for Jennifer.

"Fine, no explosions." The Captain conceded as John radioed.

"Anything?"

"Possibly. Can you get some rope?" Laura requested, having a brainwave.

"Sure, give me a few minutes." John replied before cutting the connection allowing Laura to pay all her attention to her friend. Squeezing her hand again she said.

"I'm going to have to collect the rope. I'll be right back." As she spoke she felt Jennifer tense causing her to add. "I promise I'll be back in no time and then we'll get you out." Squeezing her friend's hand once more she backed out of the space and down the shaft.

As she reached the opening she felt Ronon's hands on her as he helped pull her out asking. "How is she?"

"I can't tell, it is too small in there to move and I can't get to her gag. But she is awake."

"What's the plan?" John asked as he returned carrying rope. Taking it from him Cadman explained.

"I'm going to tie this round her legs, when I give the go ahead you guys pull her out." Seeing the doubt on everyone's face she added. "It's the only way. There's virtually no space through there."

"Understood." John nodded before informing Cadman. "Medics will be here soon."

"I'll try to beat them back." Cadman said disappearing into the shaft again.

As she reached Jennifer she tried to pass the plan onto her friend, although she wasn't sure how much Jennifer was taking in. Shaking her head she tied the rope round Jennifer's legs, which were already bound and tried to half lift half drag Jennifer back into the main shaft. With Jennifer's legs in the shaft Cadman crawled over her friend's legs further down the darkness and tried to move the rest of Jennifer into the shaft. When she was finally content she called. "Ready. Go slow."

Moments later Jennifer started to slide down the shaft with Laura following behind trying to support her head.

As soon as he could reach her Ronon used his hands to pull her free from the shaft before gently collecting her in his arms and moving to the corner of the room. As he set her down he couldn't help the anger rise in him when he saw the blood that caked one side of her head. Pulling a knife he quickly cut the ropes as John helped remove her gag.

Jennifer struggled to focus on them in the relative brightness of the room. Opening her eyes caused her head to hurt and all she wanted was to sleep. She was vaguely aware that she was being asked questions, but she didn't seem able to answer them.

The next thing she knew she found herself almost floating. Opening her eyes she saw the room and then the corridors moving. Turning her head she saw Ronon moments before she passed out.


	16. Chapter 16

"Can you remember what happened?" John asked Jennifer, who lay in the infirmary, still looking pale.

"It's all a blur." Jennifer said, frustrated with herself. "I remember going jogging, then I remember waking up in the dark." She paused shivering at the memory.

"No idea who clubbed you then?" McKay asked.

"That's kinda what she just said Rodney." Laura pointed out.

"Don't worry about it." John said to Jennifer. "It'll come back. You took a nasty blow to your head, you're also badly dehydrated so the docs warned you'd feel like crap for awhile." Noticing Jennifer's dubious look he added. "Obviously they didn't phrase it quite like that, but you get the point."

Looking around Jennifer realised they were on the Daedalus and said. "We're not on Atlantis. How did you get here?"

"Caldwell mentioned he lost you so we gated to the nearest planet and got picked up." John explained. "We'll be home soon though." He added, before trying to focus Jennifer back on the attack by asking. "Can you remember the work you were doing before you disappeared?"

"Yes." Jennifer said, not wanting to say more in the populated infirmary.

"You think there could be a connection?" John asked.

"I can't remember anything of the attack, so it's possible." Jennifer replied. "But I do remember that none of the samples I tested came back positive."

"Did anyone react badly to having the tests done?" John asked.

"Just the normal grumbling. Sorry, I'm not being much help."

"You're doing fine." John told her before adding. "We'll keep investigating. Try and get some rest." He then paused and glanced briefly at Ronon before saying, oblivious to Laura's smirk, "Until we figure out who did this Ronon is not leaving your side."

-00-

"How is she?" Caldwell asked when John's team, minus Ronon, entered the briefing room.

"She'll be okay, but she can't remember anything." John explained. "I've left Ronon guarding her."

"In that case let's focus on the air recirculation room. You said Ronon found blood on the floor?"

"Yes, but that may not have been where she was attacked." Teyla answered.

"True, but even during the night shift someone would notice her getting dragged through the ship. Even if it wasn't in that room it must have been close." Caldwell argued.

"Unless they used the transporter." McKay suggested.

"Already thought of that and checked. There is no indication that the transporter was used, or that the logs were tampered with." Caldwell answered.

"I take it there was no official reason for her to be down there? There wasn't a medical alert?" John asked.

"Negative. Not an official one anyway. Marks found no trace of any radio comms to Dr Keller. Any other theories?" Caldwell asked.

"The way I see it there are three possible reasons for her to get attacked. One someone found out she was investigating the nanites; two she stumbled across something she shouldn't; three revenge." John suggested.

"Revenge seems unlikely." Caldwell said.

"Agreed, which leaves one and two. It would be a mighty big coincidence if it weren't one, but with the doc's luck it could easily be two."

"Do you think there is any connection between this and Milton?" The full Colonel asked.

"Again, too much of a coincidence to discount." John said. "But right now I can't see a way to link all the events together. Rodney?"

"As much as I would love to prove he had something to do with this, I can't. Yet." McKay replied.

The room fell silent as everyone considered the different pieces of the jigsaw puzzle. Finally Caldwell leaned forward and said.

"Dr McKay, I want you to go through the air recirculation room and search for anything suspicious or out of the ordinary. If Dr Keller did walk in on something the evidence could still be there."

"Or hidden near by." John suggested.

"Agreed. Sheppard sweep the area and see if you can find anything."

"Are we targeting any individuals?" Teyla asked.

"Not specifically unless any of the samples Dr Keller took show traces of nanites."

"But we can narrow down the list of suspects. To get Jennifer in the blackout area they would need to be small but strong." Rodney said.

"Seeing that everyone on this ship has completed basic training the strength requirement doesn't help." Caldwell commented.

"Size may. That shaft was really tight. No way I could have fitted." John countered.

"Even if we ruled out every male of average build or above, that still leaves us with a large number of men and almost every female crew member as potential suspects." Caldwell pointed out. "So for now focus on areas rather than people." He paused before adding. "The fact they knew about the blackout area down there opens up the possibility that they have a science or engineering background. So any intel you get report in person."

"You think they're monitoring radio traffic."

"I hope not, but I can't rule it out. If the Trust are involved I know all too well the lengths they'll go to."

-00-

Hours later, growing frustrated by the lack of news, Caldwell made his way down to the infirmary to check on Jennifer. As he entered the small area he saw Davis on one side monitored by two marines. On the other side he saw Ronon standing near an empty bed. Walking over he asked.

"Where is she?"

Silently Ronon nodded towards where Jennifer sat hunched over a workbench.

"How long has she been like that?"

"Two hours."

"Why didn't you stop her?"

"She's more relaxed this way." Ronon shrugged earning a dubious look from Caldwell who walked over to Jennifer.

"Doctor."

"Colonel?" Jennifer said startled by his presence. "What are you doing down here?"

"I came to check on you."

"I'm okay." Jennifer assured him, although her bandaged wrists and head suggested otherwise.

"If that's the case why are you still in the infirmary?"

"Seeing I can't remember what happened to me the only way I'm going to be any use is to keep investigating what I was working on and look for a connection to that and the air recirculation room."

"Uh huh. Alternatively you could rest and help by recovering." Caldwell countered as Sheppard walked over to the pair.

"Doc why are you working?" He asked, throwing an almost accusatory stare at Caldwell.

"Is this double act part of Air Force training?" Jennifer asked.

"No, but apparently it should be." Caldwell said. "Tell me, have you found anything useful yet?"

"Well no but-" Jennifer started only for Caldwell to cut in.

"And the nanite tests could easily be run by Hargreves and Lang, both of whom tested negative for nanites?"

"Yes b-"

"So it's agreed you are to go to your quarters and rest." Caldwell jumped in again. "Ronon please escort Dr Keller to her quarters. Unless there is a medical emergency, or she feels worse I don't want her back in the infirmary for at least eight hours."

Jennifer opened her mouth to argue but gave up on seeing the three resolute faces before her.

"Fine. I'm going." She conceded, as she walked off, Ronon in tow.


	17. Chapter 17

As Jennifer sat in her quarters she started to grow bored and frustrated, she also started to feel very claustrophobic. Looking at Ronon she wondered if this was a good time to strike up conversation with him and try to salvage their friendship. But she couldn't think of a good way of starting the conversation so she remained silent. As the silence hung in the room the small size of the room seemed to be highlighted and Jennifer felt herself get nervous. Suddenly getting an idea she jumped up.

"Where are you going?" Ronon asked as Jennifer started to pull on her shoes.

"A walk."

"You'll be safer here." Ronon pointed out, not happy about Jennifer being out in the open.

"Firstly, whoever attacked me has gone to great lengths to keep their identity secret, attacking me in view of everyone would be stupid. Secondly, sitting here isn't helping to jog my memory, maybe if I go over the route something will come back to me."

Unable to argue with her logic Ronon stood and opened the door, asking. "Which way did you go?"

Smiling at her victory Jennifer stepped out of the cabin and started to retrace her steps.

"You used my route." Ronon commented after a few turns.

"I guess it got stuck in my mind." Jennifer said as she kept walking.

"You shouldn't have ended up near the air recirculation room." Ronon pointed out as Jennifer came to a stop.

"I know that. I think I got distracted and went that way instead." She said pointing down another corridor.

"You don't know where you ran?"

"I wasn't paying much attention. I had other things on my mind." Jennifer said walking down the corridor. Sensing Ronon rolling his eyes she commented. "Don't do that. I thought the Daedalus was safe and I was trying to get to the bottom of the problem."

"You need to be more aware of your surroundings." Ronon chastised as Jennifer paused at another junction. Setting off again Jennifer wondered why she had taken this route, but decided not to voice the question.

After twenty minutes they finally turned onto the walkway that led to the air recirculation room. Jennifer paused and glanced at Ronon, checking he was still there before nervously walking to the door. Stopping and waiting for the door to open she was grateful that Ronon stepped up beside her. As the door slid open she took a deep breath and stepped inside the now empty room. As she did so she started to have a flashback to the wrench coming down on her and instinctively she reached out and grabbed Ronon's hand.

Surprised Ronon looked at Jennifer, worried by how pale she looked, and squeezed her hand.

After a few moments he asked. "You remember anything?"

"A wrench." Jennifer said before sighing and adding. "But not who was holding it." She gazed at the room once more, trying to force herself to remember what had happened before finally giving up. It was at that moment she realised she was holding Ronon's hand. Embarrassed she pulled it away and mumbled an apology. She was momentarily saved from any further awkwardness by being summoned to the briefing room. "I should go." She said quickly, avoiding all eye contact with Satedan as she turned and headed to the door. Not knowing what to do Ronon followed silently behind.

-00-

"What took you so long?" Rodney asked when Jennifer finally reached the briefing room. "Your quarters are a two minute walk from here and yet it's taken you nearly ten minutes to get here."

"I wasn't in my quarters." Jennifer shrugged.

"I thought we agreed you weren't going to work." John said.

"Technically you agreed, but I wasn't working. I went back to the recirculation room so see if it jogged any memories." Jennifer replied.

"And?" John prompted.

"Nothing useful."

"Fortunately I have made progress." Rodney said.

"Really?" Jennifer asked, feeling more optimistic.

Before Rodney could start an explanation John looked at Ronon, who waited by the door and said.

"Get some rest. I've got her."

Knowing John meant it as an order Ronon reluctantly left the room.

"What have you found?" Jennifer asked sitting.

"A loose part." Rodney said triumphantly. "Whomever you disturbed was rattled enough not to cleanly finish what they were doing. They ended up not properly securing a panel. Behind that panel was a new part that they hadn't installed properly."

"What kind of part?" Jennifer asked.

"An air filter."

"I was knocked out over an air filter?" Jennifer asked.

"Of course not." Rodney said, annoyed she hadn't realised where he was heading.

"The air filter is a common part both here and on Atlantis. It effectively cleanses the air chemically." John said. "Inside each one is a canister of various gases. Only in this one there wasn't the normal gases."

"What was in there?"

"Nanites." Rodney answered.

"Nanites? They wanted to assimilate the ship and Atlantis?"

"No, I don't think so. That's far too risky, even for the Trust." Rodney said.

"So why release them?"

"We were hoping you could tell us." John said. "Say Davis is innocent, they could have used him as a lab rat."

"Makes sense to have a pilot study." Jennifer agreed. "But the nanites in his system weren't active."

"The ones in the canister are." Rodney said.

"Can you tell what they're programmed to do?"

"I'm trying to decode their program now. So far all I can work out is they were to go to the brain stem."

"Any ideas why?" Caldwell asked sitting forward.

"From there they could do anything." Jennifer said. "I'm going to need more information."

"Or a test subject." John said.

"You can't be serious." Jennifer asked.

"When we catch who attacked you, if they won't talk it may be our only option." John said.

"When you say anything, could you be more specific?" Caldwell asked, keen to learn of the different possibilities.

"Not really, but the obvious examples are: death, some sort of virus, physical or mental modifications." Jennifer started to list only for Caldwell to interrupt asking.

"It is possible that they could take control of the subject?"

"Theoretically yes. We have come across plenty of technology that would allow a certain degree of mind control, especially when combined with nanites. But the technology and research is locked down, very few people would have access. And even fewer would have access to all the different elements." Jennifer argued. "Until I get more information about these ones there is not much I can tell you."

"Dr McKay," Caldwell said, "I want that code cracked."


	18. Chapter 18

Making best use of Jennifer's meeting Ronon went to the gym, hoping Teyla would be there for sparring practice. Instead he found the sole occupant was Cadman who was busy attacking a punch bag. Entering the room he started to walk over to another punch bag only to stop when Laura spoke.

"You know what the problem with smart people is?" Cadman asked, turning to face Ronon. For a moment Ronon raised an eyebrow wondering why Cadman was talking to him. Eventually though he said.

"Lack of survival skills."

"Not was I was thinking, but good point. Do you know what the other problem is with smart people?" Cadman responded, seeing Ronon was about to answer she went on. "That one's rhetorical. Anyway the other problem is sometimes they do really dumb things. Take Jennifer for example, she got scared and rather than taking time to think or to talk she just made up an excuse and ran a mile."

Ronon wasn't sure where Cadman was going with the conversation but he optimistically looked at the door hoping Teyla would enter.

"So sometimes less smart people like you and me have to read between the lines and give her another chance." Cadman said, hoping he would catch onto what she was saying. When it became obvious he was completely lost she said.

"For the record I've not told you this and if you ever tell Jennifer I have told you I will hunt you down." Cadman threatened causing Ronon's eyes to twinkle in amusement. "I'm serious. I can do things with explosives you can only dream of." Laura went on. Finally happy she was being taken semi seriously she said.

"She lied."

"Who lied?" Ronon asked.

"Jennifer?" Laura explained causing Ronon to jump to conclusions.

"She knows who attacked her?" The Satedan said tensing.

"No. That's not what I'm talking about." Cadman said, seeing Ronon relax again she went on. "When she said she was interested in someone else, she lied. She wasn't. She's interested in you, but she got scared and lied. So it's up to you to sort it out."

"Me?" Ronon asked, still trying to take on board what Laura had said.

"Yes you." Laura said turning to leave the gym.

-00-

An hour later Ronon was still stood in the gym trying to process what Laura had said. He was so caught up in his thoughts he didn't even register the gym doors open and two bemused people walk in. He was finally startled from his thoughts by John almost shouting.

"Chewie!"

"Sheppard." Ronon managed to respond.

"You okay buddy, you looked like you were on another ship?" John asked, concerned.

"Fine."

"What were you thinking about?"

"Jennifer." Ronon said without thinking. On hearing her name Jennifer misinterpreted Ronon's meaning and said.

"I'm okay. Besides Rodney is making headway."

"He is?"

"Yes." John confirmed. "We think we have a why, or at least half a why and that may lead to a who. I need to help Rodney check some records, so in the mean time you're in charge of the doc's safety." He added before looking at Jennifer and saying. "And she's still banned from the infirmary for at least three hours." With that he turned and left.

"Your quarters?" Ronon asked.

"I guess." Jennifer said reluctantly.

"You'd prefer to spar?"

"I think I have enough bruises." The doctor replied.

"Let's go then." Ronon said leading Jennifer out of the gym and down to her quarters, trying to forget what Cadman had told him.

"You okay?" Jennifer asked, sensing his unease.

"Fine." He said gruffly enough that Jennifer did not peruse the conversation further.

When they finally reached Jennifer's quarters the doctor stopped in the doorway, sensing something was wrong.

"What's wrong?" Ronon asked sensing Jennifer tense.

"Something seems different." Jennifer said. "Probably just my imagination."

"Trust your instinct." Ronon instructed as he looked round Jennifer's quarters, searching for anything sinister. "What's out of place?"

"I can't put my fing- The bed! The sheets have moved at the far end by the locker. See." She said pointing to the corner of the bed. "I can never get my corners looking so neat. Someone has been in here and made the bed. Did that sound as stupid as I think it did?"

Concerned Ronon carefully moved round the room looking for anything sinister. Stopping he asked. "Anything missing?"

"I put everything away in my locker. Including my computer, with the blood results." Jennifer said, jumping to the conclusion that some one had been looking for her work. Instinctively she started to move away from the doorway and reach out to the locker, intending to search it, only for Ronon to grab her bandaged wrist and pull her arm back. Seeing her wince he apologised before explaining.

"They could have set a trap."

Nervously Jennifer inched away and stood back in the open doorway as Ronon carefully looked at the locker. Not seeing any wires he told Jennifer to stand back before he carefully opened the door.

As the door swung open Jennifer felt her heart rate increase, but as she peered into the darkened locker and saw no sign of traps she allowed herself to relax.

"Sorry, must just be me loosing my mind." Jennifer said stepping inside her quarters. As the door started to shut behind her she suddenly saw Ronon launch himself at her, pushing her through the doorway then half drag, half pull her down the corridor. Before she could even start to react to what was happening an explosion tore through the corridor knocking her and Ronon off their feet.


	19. Chapter 19

"What the hell was that?" Caldwell demanded as the Daedalus rocked.

"There has been an explosion on deck twelve. We have a hull breach." Marks explained as he scanned the screen for more information. "Automated emergency procedures have initiated. All bulk heads have sealed and the breach is contained."

"Were we hit?" The Colonel asked.

"Negative, all scans and radars did not show any projectile or another ship. Shields are still in tact."

"What blew? There aren't any engines on deck twelve."

"I don't know Sir. The breach is in the crew quarters."

"Was anyone down there?" Caldwell asked concerned.

"Currently unknown. I'm trying to pull up the sensor information from just before the explosion, but the wiring has taken too much of a hit."

"Are we under attack?" John asked sprinting onto the bridge.

"It seems not. Looks like it was an internal explosion." Caldwell explained as McKay took control of Marks's station. After a few moments he exclaimed.

"Jennifer."

"What is McKay?" John asked.

"The explosion originated from Jennifer's quarters."

Instantaneously John reached for his radio and desperately tried to reach Ronon and Jennifer, only to get silence as a reply.

"Rodney with me." John ordered as he hurried down to deck twelve.

-00-

As the shock wore off Jennifer started to look round, searching for Ronon. Seeing the big Satedan lying to her right she called to him before getting to her feet and stumbling over. As she reached him she was relieved to see him stir. Dropping to her knees she tried to hold him still as she searched for injuries as he tried to shake off her attention.

"I'm fine." He said gruffly as he got to his feet.

"What exactly happened?"

"Bomb." Ronon replied succinctly.

"How did you know?" Jennifer asked.

"I saw wires round the door and guessed." Ronon explained as he walked towards the far bulkhead, which was sealed. When his attempts to open it failed he turned and asked. "You have your radio?"

"No. It must have come off just before the explosion." Jennifer replied.

"Mine too. You know how to do stuff and get the radio working." Ronon said pointing to a blown speaker on the wall.

"As in do I know how to rewire, or re-crystal the circuits to turn them into a working radio?" Jennifer asked.

"Yeah."

"No." Jennifer replied as Ronon tried to force the bulkhead. "But I could try." She shrugged removing a nearby panel and scanning the contents. "But you do realise I'm just as likely to deactivate life support as I am to get a radio link?"

"You can do it." Ronon said.

"As much as I appreciate your groundless faith if this all goes wrong I'm sorry."

For the next ten minutes Jennifer looked at the crystals, removing some and turning others before finally giving up. "It's no good the ones I think we need are too badly damaged." Sighing Jennifer walked up to the bulkhead and slid down to the floor saying. "Here we are again."

"No oxygen tanks this time." Ronon said sitting down next to her.

"Probably a good thing. Explosions in ships are bad things." Jennifer replied as she started to play with the bandage round her left wrist.

Thinking back to what Laura had said Ronon knew that this was a perfect opportunity to talk to Jennifer, but no matter how hard he tried to come up with something to say, he couldn't. Growing frustrated with himself he stood up and paced the small section they were trapped in. Each time he paced from one side to the other in only a few strides it highlighted to Jennifer how small the area was, making her remember waking up in the darkened shaft she had been trapped in. As the memories flooded back she started to feel anxious. At first she fidgeted, then she sweated, then she fidgeted some more as her mind became fixated on the near walls that seemed to be getting even closer.

"You okay?" Ronon asked when he noticed her strange behaviour. When she didn't respond he kneeled in front of her and shook her shoulder, causing Jennifer to jump.

"Sorry?" She asked distractedly.

"You okay?" He repeated, mentally kicking himself for asking such a stupid question.

"Yeah." Jennifer said, her voice lacking conviction. When Ronon continued to stare at her she confessed. "Apparently my time tied up in the shaft has made me a bit claustrophobic. I'll be okay."

"Can I help?"

"Short of opening the door, probably not. It's kinda mental thing. I'll just have to work through it and not concentrate on the walls, or how close they are." She smiled weakly.

"So you need a distraction?" Ronon said.

"What did you have in mind?"

"We could talk." He offered.

"Okay. About what?" Jennifer asked as she went back to playing with her bandage.

"You?"

"Me? Not really an interesting subject." Jennifer said killing the conversation. Frustrated Ronon moved so he sat next to her and tried to think of something else to say. It was Jennifer though who eventually broke the silence.

"You were right." She paused and for a moment Ronon thought she wouldn't add to her comment, but then she said. "About me being weak. You were right. I'm not only weak, I'm a coward. First sign of something different or confusing and I ran."

"You're not a coward." Ronon assured her. "And you're not weak."

"Really? What would you call lying and running a mile?" Jennifer asked.

Hoping she was referring to their conversation a few weeks ago when she said she was interested in someone else he said.

"Complicated."

"Story of my life." Jennifer said before turning to look at Ronon and saying. "I'm sorry. I never meant to hurt you and I never wanted to jeopardise what we had."

"Do I scare you that much?"

"No of course not. I could never be scared of you. I know you would never do anything to hurt me. I was scared of me, of what I would do or could do. I was confused and didn't know what I wanted and couldn't make a decision so I ran."

Hearing enough Ronon started to lean towards Jennifer, pleased when she mirrored his movements. They were just about to finally kiss when the bulkhead door started to move. Not expecting the movement they both jumped apart before falling backwards as the door effectively disappeared.

"Sorry, should have knocked." John said looking down at them. "You two okay?"

"I guess." Jennifer said sitting up with Teyla's help.

"What happened?"

"There was a bomb in my quarters. Ronon spotted it just in time to get us out of there." Jennifer explained as Ronon helped her to her feet.

"A bomb?" Rodney asked before adding. "You should really come with a health warning."

"Thanks Rodney."

"Can you describe the bomb?" Laura asked.

"Yes." Ronon replied immediately.

"First things first, both of you go to the infirmary and make sure there's no damage. When you have the all clear work with Cadman, let's see if we can figure out who is behind this. In the mean time we'll look into the ship's supplies and see if any explosive material is missing. Teyla, Ronon, the doc is not to be left alone." John ordered, wondering where the next threat would come from.


	20. Chapter 20

"What do you have?" Caldwell asked.

"I can't be one hundred percent sure as the actual bomb evidence is floating somewhere in space right now, however, based on what Ronon and Jennifer said I confident whoever did this was a pro. The way the bomb was rigged, to go off on the closure of the door, was well thought through."

"In what way?" John asked.

"Well Sir, it helped keep the explosion contained. If the door had been open the damage would have been far worse, possibly taking out the entire ship."

"So your belief is the Daedalus was not the target?" Caldwell questioned.

"Correct Sir. Based on my guess for how much Semtex was used if they wanted to blow the ship they could have easily done so by placing the Semtex near the generator."

"How do you know it was Semtex?" Rodney asked.

"There's some missing."

"Any suspects jump out at you?" John asked.

Laura glanced at McKay and sighed.

"Well Sir, to save Rodney the effort I may as well forward my name. I'm an explosives expert and proved I'm small enough to fit in that shaft."

"I didn't say anything." Rodney protested.

"Do you remember trying to kill the doc twice?" John asked.

"No Sir."

"Seeing how your blood work came back nanite free I'm pretty sure we can discount you." Caldwell said. "So who else?"

"Hard to say without seeing everyone's files." Laura said.

"Can you give us a list of what to search for?" John questioned.

"Yes and no. For military personnel it will be relatively easy, but for the civilian staff the info might not be in the files anyway, even if it is it won't be so obvious."

Tapping at a screen Caldwell said.

"Ignoring Drs Keller and McKay, as well as Ronon and Teyla we have twenty-two civilians on board. Six of whom are women." He then looked at Cadman and said. "I'll authorise you to access all files. Search for anything that make them a promising suspect. Start with the civilians then move onto military."

"Yes Sir."

"That'll be all."

"Sir." Laura responded before standing to leave the room only to be called back by John.

"Cadman, it may be worth showing the doc any photos you have of the suspects, it may help to jog her memory."

"Yes Sir."

-00-

"You should try to rest." Teyla told Jennifer, who paced in her new cabin.

"A few too many distractions to do that." Jennifer said glancing over at Ronon. Looking back at Teyla and sensing an argument she conceded. "I'd get something to eat though."

"Good. I'll fetch something." Teyla offered.

Jennifer considered the offer and part of her wanted to accept so she could talk to Ronon alone, but the confinement was still making her nervous so she said. "Actually I'd prefer to go. I wouldn't mind being in a larger space."

"You'd be safer here." Teyla pointed out.

"I know, but I really need the walls less close."

Unconvinced Teyla looked at Ronon who nodded his approval causing the Athosian to say.

"Very well."

"I'll take her." Ronon offered.

"Should we not both go?"

"No. Last time they placed a bomb in her room when she wasn't there. They could put another in here. One of us should stay and make sure they don't."

"I'll stay." Teyla offered, not entirely convinced by Ronon's argument but sensing that the other two needed to talk without her there.

"Thanks." Jennifer said warmly as Ronon led her out of the room.

"Ronon?" Jennifer asked as they walked down the corridor.

"Yes."

"I know now isn't the right time, but I don't want it to be like last time. I don't want us to pretend it didn't happen, well nearly happen. What I mean is-" She was cut off my Ronon saying, as he took hold of her hand.

"I know. We'll talk when it's over."

As they entered the mess hall Ronon released Jennifer's hand. As he did so Jennifer was surprised with how noticeable the lost contact was.

As Ronon lead her towards the food Jennifer glanced round the mess hall trying to identify an out of the way table. As she scanned the room she caught a glimpse of one of the science team. It was someone she didn't know, but recognised.

"You okay?" Ronon asked noticing Jennifer was distracted.

"I," Jennifer started as she started to remember what happened in the recirculation room. "That's her." She said pointing to the scientist.

Not questioning Jennifer, Ronon started to move towards the scientist. However, his sudden movement alerted the woman to his intentions and just as a marine cut across Ronon's path the scientist bolted towards the exit only to go flying when she tripped over Jennifer's outstretched leg.

As several marines secured the scientist Ronon noticed Jennifer was rubbing her shin, causing him to ask. "You okay?"

"Yeah, I just didn't realise that tripping thing is so painful. It looks really easy in films."


	21. Chapter 21

"Who are you working for?" John asked again, loosing patience. "Work with me Huntley and you'll be spared justice Atlantis style."

"We both know you can't do anything to me. You can't prove I've done anything."

"Dr Keller has identified you as the one who attacked her." John pointed out.

"Her word against mine."

"Why would she lie?"

"She's mistaken, or she is worried by my success or she has been taken over by some alien entity. No too clichéd. But while we're working down that list how about jealousy? She thought I was making a move on McKay, or you or, I know, Ronon." Huntley smiled.

"And your fingerprints on the air filter were part of her elaborate plan to frame you?" John asked, smiling when he noticed the surprise on Huntley's face. "That's right, we found the filter and the canister with the nanites. We also have you leaving the armoury an hour before Dr Keller's quarters were blown up with Semtex stolen from the stores. We have enough to convict you in both Galaxies. So who are you working for?" When John was again met by silence he changed his line of questioning. "Fine we'll leave that one. What are the nanites programmed to do?" When he was again met by a stony silence he said. "We will find out and there are three ways that will happen. One Rodney cracks the code, two you tell me or three we test it out on a live subject. Want to guess who that subject is?"

"You wouldn't." Huntley replied.

"You sure about that? I've done worse. So has Ronon." John countered before changing his line of questioning again. "How about this one, why not just kill Dr Keller? Why knock her out, drag her through the ventilation system and tie her up, then try to blow her up? Why not just kill her?"

"I'm thought I had killed her. I didn't think she'd survive the blow. But I hit her as I panicked, not because I wanted her dead. When I realised she wasn't dead I couldn't kill her, I'm not a killer." Huntley explained.

"So instead you dragged her down a shaft, where you knew the sensors wouldn't work and left her to die?" John asked angrily.

"What choice did I have? I couldn't risk getting caught."

"Where does blowing her up feature on your no killing mentality?" John questioned.

"I had my orders."

"From who?" John asked, concerned she had received orders whilst on board. As Huntley remained silent Caldwell entered the small temporary interrogation room.

"Sheppard this is too slow." The Colonel greeted. "We are nearly at Atlantis. You have permission to proceed with your backup plan."

"You sure?" John asked.

"Don't go soft on me now Colonel." Caldwell replied. "Dr McKay has set up a completely isolated room. When Huntley is relocated there you can release the canister with the nanites."

"I know you're bluffing." Huntley said calmly.

"Dr Huntley," Caldwell said. "Your file indicated you have never been to Atlantis."

"So?"

"So, there is a lot you don't understand, things operate a little differently over there. Didn't your Trust friends tell you what happened last time they tried something big? No? Let me fill you in. Permission was given to have Dr Kavanagh tortured by Ronon, which ended with the scientist unconscious on the interrogation room floor." Sensing he had her attention he went on. "I won't even tell you what happened to me. Needless to say over here, out of the reach of the IOA, different rules apply. Right now my sole concern is the protection of this ship and Atlantis and I will do anything to achieve my goals, including endorsing Colonel Sheppard's science experiment." He paused as he walked round behind her. "I'll admit I had my doubts, not about subjecting you to the nanites, but whether we'd learn anything. You see I was thinking that what ever you were doing on board the Daedalus would affect you too. So why would you worry if we gave you the nanites. Then Dr McKay suggested an intriguing hypothesis, that the nanites here had different programmes to those for Atlantis. And you're not due to stay on Atlantis are you? So while you may have been prepared to get infected with the nanites destined for the Daedalus, you probably aren't for the Atlantis bound ones." He walked round to Sheppard and added. "Then again maybe Dr McKay is wrong. I guess we'll find out soon enough." With that he nodded to two marines who stepped forward and grabbed Huntley by her elbows, pulling her to her feet.

"You're bluffing." She said, sounding less sure than before as she was led from the room, Caldwell and Sheppard following behind.

When the group reached a cargo hold the marines paused briefly to open the doors before pulling Huntley inside. Once inside she saw a small room and McKay, who was frantically typing away.

"Are you ready Dr McKay?" Caldwell asked.

"I think so."

"Think so or know so?" Caldwell asked. "I want you to be damn sure the nanites can not escape."

"I'm sure." McKay insisted. "That room is completely sealed and surrounded by a nanite proof forcefield. If the worse did happen, we press that button," he paused and pointed to button to the side of the room, "and everything inside gets incinerated, including the nanites."

"Shouldn't it be a big red button?" John asked.

"Working to a really tight timescale here. Next time I'll stop what I'm doing and run out to Radio Shack and get a big red button for you." McKay sniped.

"Are you sure you're ready?" Caldwell cut in impatiently.

"I'm sure."

"Good." The full Colonel said turning to Huntley. "This is your final chance. Are you ready to cooperate?"

"You're bluffing." Huntley said.

"I'll take that as a no. Seal her in." Caldwell ordered just as Jennifer stormed into the cargo bay.

"Tell me you're not doing this." Jennifer demanded.

"It's the only way." John shrugged.

"It is completely unethical."

"Huntley tried to kill you, twice." John pointed out.

"Does that mean we should stoop to her level?"

"Doctor." Caldwell said calmly. "We are not clear what her endgame is. It could well be the destruction of Atlantis. Far more lives are at stake than Huntley's."

"So that's it? Out with morals and ethics? Why not feed her to the Wraith while we're at it in exchange for a meal with Todd?"

"Doc-" John started only for Caldwell to interrupt.

"Doctor, I understand why you feel uncomfortable with this, which is why we have kept you out of the loop. However, I am in charge and I have ordered this course of action. We will infect Huntley regardless of your opinion."

"You can't do this." Jennifer protested.

"Ronon, please escort Dr Keller to her quarters." Caldwell ordered.

The former runner looked to John who nodded causing Ronon to tug the still complaining doctor to the door.

When the din had finally silenced Caldwell looked at the marines and a pale Huntley ordering. "Seal the door."

The door was an inch away from being shut when Huntley cried.

"Wait, I'll talk."


	22. Chapter 22

"Doc that was great." John said entering her temporary cabin. Seemingly oblivious to her death stare he went on. "We could not have done that without you."

"Don't you dare blame me for torturing her." Jennifer said seething.

"Who's being tortured?"

"Fine experimented on."

"Doc, no one is experimenting on anyone." John said raising his hands in a defensive gesture.

"So what would you call it?"

"Bluffing." John said, his answer leaving Jennifer momentarily speechless, allowing him to explain. "We never had any intention on exposing her. But we needed her to believe we did. So we let you believe we were going to release the nanites so you'd come in and be a little….tetchy. It worked, Huntley was convinced we were going to expose her and talked."

"You couldn't have told me this first?" Jennifer asked.

"Doc, Lorne has told me how bad you are a poker. We needed you to be as believable as possible." Ignoring Jennifer's glare John went on. "However, I'm afraid I'm the bearer of bad news."

"How bad?" Jennifer asked, still annoyed with John.

"Huntley has admitted to rigging the air filters and attacking you. She also confessed to the bomb, however, she says the bomb was done to follow orders she received yesterday."

"So she's not working alone?" Jennifer guessed.

"Looks that way. Although there's no need to keep you silent or to prevent you remembering anything, you could still be a target."

"You mean your threats weren't enough to give you the other or others?" Jennifer asked pointedly.

"She claims she doesn't know."

"You believe her?" Ronon asked surprised.

"Jury's still out. However, it makes sense for the Trust to keep a level of anonymity between the different operatives, just in case we caught one. Also she has been free flowing with other information."

"So what were the nanites for?" Jennifer asked.

"The ones on the Daedalus were a final test. They would have been released, infected everyone, then deactivated."

"Like Davis?" Jennifer asked.

"Yes, apparently he was infected during his leave. When he was cleared for duty they implemented the second phase, the filters on the Daedalus. If the Daedalus got to Atlantis phase three would have been rolled out."

"Which was?" Teyla asked.

"Which is unknown. Huntley was told that if she wanted to live she should make sure she was on the return trip."

"So we still don't know anything." Ronon pointed out.

"I wouldn't go that far. McKay also has some more ideas. But until we know more we have to assume you're still in danger." John said looking to Jennifer.

"So I'm under guard until we get to Atlantis. At least we're not far off." Jennifer said. The remark causing John to pull a face and say.

"I appreciate you want off the ship, but it has been decided that until we know what the nanites were for and discovered who was issuing the orders, the Daedalus is to be quarantined. No one will be getting off at Atlantis."

On hearing the news Jennifer side stepped John and reached for the door.

"Doc, the whole you being at risk thing should have been translated as you need to stay here."

Spinning round, still angry at John's earlier stunt she said.

"If they really want to take me out they'll find a way to get to me. In the mean time I'm going to be more use in the infirmary than I am here." With that she turned and left, Ronon following silently behind.

"She's ticked." John said as the door closed.

"And you always say you're not good at reading emotions." Teyla smiled.

-00-

"Did you know?" Jennifer asked as she marched towards the infirmary.

"No."

"Would you have told me if you had?"

"If Sheppard had ordered me not to?" Ronon countered.

"You're right it was a stupid question." Jennifer said before she felt Ronon's hand on her shoulder as the Satedan turned her.

"If you would have been in danger I would have told you." He assured her before adding. "Sheppard did what he thought was for the best."

"I know and I accept that. But it doesn't mean I can't feel annoyed." Jennifer replied looking up at Ronon. "I'm sorry, I didn't mean to have a go at you." Just as she found herself getting mesmerised by his eyes two marines jogs passed jostling them, breaking the moment before it began.

"We should go." Jennifer said. Reluctantly Ronon turned away from Jennifer and started to walk by her side towards the infirmary.

"Would you feel better if you stunned him?" Ronon asked.

"Sheppard?"

"Always works for me." Ronon shrugged. "You can borrow my gun."

"I appreciate the offer, but I'm sure I can come up with something better." Jennifer replied.

As they entered the nearly deserted infirmary Ronon said.

"They don't train enough here."

"Or perhaps they just train more carefully." Jennifer replied as she made her way over to a workbench where the latest results were waiting.

As she looked over Davis's scans something jumped out at her. She quickly pulled up other results and the blood work. Growing excited she reached for her radio and tried to get Rodney.

"McKay here." Was the terse reply.

"Rodney, it's Jennifer. Can you meet me in the infirmary?"

"Now?" Rodney asked annoyed.

"Yes now. It's important." Jennifer said not wanting to say too much over the radio link.

"Important as in physics or important as in how a biologist views their work?" McKay questioned.

"Rodney please just get here."

"Fine, I'm coming." Rodney relented.


	23. Chapter 23

"What's going on?" John asked as he and Caldwell entered the infirmary.

"Jennifer found something, then they started talking." Ronon summarised, nodding to where the two scientists were working.

"What kind of something?" Caldwell asked.

"Don't know, but they both seem excited by it." Ronon shrugged.

"She calmed down enough for me to go over?" John asked.

"No." Ronon replied. "She turned down the chance to stun you."

"Thanks for having my back." John said sarcastically. "But not wanting to stun me is good."

"Not really, she said she'd think of something better." Ronon said just as Rodney noticed John and Caldwell.

"Oh good, you're here. I was just about to call you. I'm going to need a few marines and Ronon."

"Why?" John asked.

"Because I'm about to identify who is behind this and I'd prefer not to end up as a target."

"How are you going to identify the who?" Caldwell asked, impatient at the lack of information.

"Well, the thing that didn't make sense to me is how whoever was in charge would know that the nanites had done what they were meant to do. I mean even if the filters had been put in place if all the nanites were meant to do were infect and deactivate, how would anyone know that had happened. That made as much sense as Milton putting Zelenka in charge. Then Jennifer found this." He said handing a tablet to Caldwell who raised a questioning eyebrow.

"It's a scan from Davis. You can see some interference." Jennifer explained.

"That's not exactly uncommon." Caldwell pointed out. "There's lots of RF equipment on board."

Moving between Caldwell and John, Jennifer touched the screen and changed the display so it showed another scan. "That one is from six hours later, still some interference." She then changed the display again. "That was from ten hours ago."

"That's a huge spike." John said noticing the interference band. Jennifer then loaded up a final image.

"This one is from ten minutes ago. No interference."

"You think the nanites were causing the interference?" Caldwell guessed.

"In a way. I believe the nanites were sending messages to someone or something and we detected that as interference. That big spike corresponds to when the nanites deactivated. A final shout if you like before silence."

"Can you use the scans to work out what the nanites were communicating?" Caldwell asked.

"It was a short repeated message. I'll need more time to figure out what exactly." Rodney said.

"So how does any of this help us?" John asked.

"Whoever is behind this on the Daedalus would have been listening for the signal. We now know the frequency and modulation of the signal." Rodney explained.

"Won't their receiver be passive?" Caldwell asked.

"In the traditional sense yes, but if I do this right I can send out a signal that will cause their equipment to resonate and we can then lock onto that."

"Possibly." Jennifer interjected.

"Why possibly?" Caldwell questioned.

"This will only work if they have the type of radio I think they have. But to avoid suspicion they wouldn't risk bring onboard anything that stood out, so I'm pretty confident my assumption is right." Rodney explained.

"And if you are wrong? What happens then?" The Colonel asked.

"Best case nothing, worse case is they'll know we're onto them."

Caldwell took two seconds to consider what he had heard before saying.

"Do it."

"I suggest we set it up in the briefing room and use that as out command centre." Rodney said. "Once we have a signal I'll direct everyone we trust down to the right area."

"Agreed. Ronon you're part of the tac team. I'll look after Dr Keller in the briefing room." Caldwell said.

-00-

"You ready yet?" John asked.

"That's the tenth time you've asked." Rodney snapped.

"Sixth." Ronon stated.

"I'm only asking as you said you were nearly done an hour ago." John replied.

"Had you not kept interrupting I'd have been done sooner." McKay shot back. "Okay. When I press the button the signal will transmit. If it does what I think it'll do we should see a spike on the scanners. When I detect it I will lock down the room where it is coming from whilst you go down and do what you need to do."

"I know the plan McKay, I came up with half of it." John said irritably.

"Does that mean you're ready?" Rodney asked.

"Been ready for the last hour." John replied.

"Okay, here we go." McKay said pressing the button as everyone stood round and watched the screen waiting. As soon as it started flashing McKay started tapping at his keyboard.

"Deck 9. Section 5. Cabin belongs to a Captain Matthews."

"Let's go." John said as he, Ronon, Teyla and Cadman sprinted from the room.

"Do you know him?" Jennifer asked Caldwell.

"Matthews? Not well. Comes from a military family and is, correction was, something of a high flyer. Personally I couldn't see why, but perhaps that's why I'm a Colonel not a General. As soon as we have him I want you to run every test you can think of to see if there is any external influence."

"Other than money." Rodney chipped in. Noticing the look Caldwell was giving him he asked. "What? Let's face it, the Trust are after power. You can't have power without money. So in the end they are all driven by money."

Before Caldwell could respond John radioed.

"We're in position."

"Colonel, may I remind you bullets and walls inside a pressurised ship don't mix well. Try not to turn my ship into Swiss cheese."

"Understood." John radioed back causing Caldwell to nod to McKay.

"Door opening in three, two, one."

Caldwell, Jennifer and Rodney stood in silence waiting for news of what was happening. After what seemed like an eternity John finally radioed.

"We have the suspect and are bringing him to the infirmary. McKay you'd better get down here, there is stuff in here you need to see."


	24. Chapter 24

"You have no idea what you've done." Matthews said from his chair.

"Stopped you destroying Atlantis?" John guessed.

"We are trying to protect Earth." Matthews said.

"We? As in the Trust?" John asked.

"Who else would have the resources to save the Earth?"

"How exactly were you planning on doing that?" John asked.

"By destroying Atlantis and all information that could lead the Wraith to Earth. Don't you see we are the ones who strive to protect Earth and uphold the original purpose of the Stargate Programme?"

"How?"

"The purpose of the programme was to explore and find technologies that could be exploited for the benefit of Earth. Yet Pegasus is a backwater. The people have no skills or technology. Our resources are being wasted. Worse than that you have alerted the Wraith to our existence. You must be stopped before you end life on Earth and the Milkyway."

-00-

"I have run every test I can conceive of and all of them come back negative. If he is being controlled by something it is something I can't detect." Jennifer said walking over to Caldwell, who watched the interrogation on a screen.

"So definitely no snake?" Caldwell asked.

"Definitely no snake." Jennifer confirmed. "And no nanites."

"Part of me was hoping there would be." Caldwell said. "It'd be easier to understand how he could have become so twisted. It sounds more like an attempt to convert Sheppard than an interrogation."

"Has he said anything useful?" Jennifer asked.

"He's said plenty. As to whether any of it is useful or even the truth only time will tell." The Colonel said as McKay bustled in saying.

"Good news and bad news."

"Good news." Caldwell asked.

"Matthews had a whole bunch of IT equipment in his quarters. Hidden on Matthews laptop was the encryption algorithm that was used on the nanites. With it I have managed to unencrypt the base code and know exactly what they were programmed to do."

"Which was?"

"The ones for the Daedalus were, just as Huntley said, designed to infect us, then deactivate and decay."

"Why?"

"See that information is not actually in the base code." Rodney said, but on seeing Caldwell's scowl he added, "however, based on one of the reports on Matthews' computer I would say that it was a final test to ensure that the shut down routine worked. The Trust seemed really paranoid about using nanites and wanted to be as sure as possible that they were completely controlled."

"So what was planned for Atlantis?" Jennifer asked.

"The nanites were to try to take control of each host. Once the nanites were in control of the host they would make them do everything possible to destroy not only Atlantis, but every record of Earth. Stage one was to wipe everything and stage two was to initiate the self-destruct. Any nanite still functioning after five days would then shut down and decay, leaving no trace of their existence or Atlantis or Earth."

"You know what worries me about this?" Caldwell asked. "The fact they were testing the deactivation and decay part. That implies the mind control, or whatever you want to call it, has been perfected already." The Colonel let his sombre statement hang in the air a few moments before asking. "Is there any sign he was not working alone?"

"No. I've found the message he sent to Huntley and Huntley is the only person he has contacted whilst on board. All indications are he and Huntley are the only operatives on board."

"So what's the bad news?" Caldwell asked.

"I've run out of my coffee supply and sugar."

Unimpressed with Rodney's answer Caldwell went back to watching the interrogation.

-00-

"You look like a marine on a mission." John said when he saw Cadman hurrying down a corridor a few hours later.

"Yes Sir, I'm trying to find Jennifer."

"You've lost her again?" John asked, wondering how anyone could be so jinxed.

"It's starting to look that way, she's not in her quarters or the infirmary or the Mess." Cadman said, clearly anxious.

"Is Ronon not still with her?" Teyla asked.

"Could be, I've not seem him either." Laura replied. "Neither are answering their radios."

"Well we're on our way to meet Ronon in the rec room now for a movie. Hang on a sec." He said as he reached for his radio.

"McKay, this is Sheppard."

"What is it now?"

"Are the ship scanners all up and running?"

"Should be, why?"

"Can you scan the rec room and tell me if anyone is there?"

"This had better be urgent." McKay muttered. After a few seconds he said. "Two life forms. Give me a minute and I might be able to tell you who…..It's Ronon and Jennifer."

"Thanks McKay." John said gratefully.

"Any other menial tasks you want carried out?" McKay asked.

"I'll let you know." John replied killing the connection.

"Mystery solved. They're both in the rec room. Why don't you join us for the movie?"

"Thank you Sir." Cadman said gratefully as she fell into step next to John and Teyla. "Rodney not coming?"

"No, he's either feeling as under appreciated as the nine button on a microwave or as overworked as most similes." John explained before saying. "I forgot to say congratulations on your new posting."

"Thank you Sir."

"You do realise that keeping the doc out of trouble is going to be one of your assignments."

"Yes Sir, but at least it's not paperwork."

"True." John said reaching the rec room and opening the door.

As they entered the rec room they all did a double take when they saw Jennifer and Ronon sleeping entwined on the couch.

"That's different." John eventually said quietly, so not to wake the pair as he strode into the room. As he did so Ronon started to stir. Noticing his friend was awake John asked as he sat on another couch. "Something you want to tell us?"

"No." Ronon whispered, checking Jennifer was still asleep.

"I'm glad you listened." Cadman whispered grinning before threatening. "Just don't hurt her."

"Captain." John said. "Do you have something to tell us?"

"Um, no Sir."

"In that case if you've finished threatening my team member feel free to start the film."


	25. Chapter 25

"Welcome back." Woolsey said as Sheppard's team, Jennifer and Woolsey beamed into the control room.

"Woolsey." Caldwell replied.

"It certainly sounds like you've had an interesting trip. Dr Keller are you recovered from your experiences?"

"I'm fine." Jennifer assured him.

"Excellent. In that case perhaps we should go to the briefing room." He suggested walking off.

"Don't look so enthusiastic." John told Ronon. "It's not like you have plans, or is it?" He asked looking at Jennifer who reddened. The comment earning him an elbow in the stomach from Teyla.

Watching from the sidelines and unaware of what was going on, Caldwell shook his head at John's team's lack of discipline before following Woolsey into the briefing room.

"I've read the report you sent." Woolsey started when everyone was seated. "How sure are you that the situation has been contained?"

"Depends on your definition of situation." Caldwell said straightening his sleeve. "In terms of the plot with Matthews and Huntley I think we are all fairly confident that it is contained. However, the Trust clearly has access to nanites that they believe can cause a level of mind control. They could try again at anytime."

"It's going to be even easier with the Ivangorod." John pointed out.

"Is there anyway we can reduce the risk? Perhaps by detecting the nanites?"

"I will add the nanite test to the standard test we run on all personnel." Jennifer said. "That will tell us if anyone is infected. But I can't stop them being infected."

"Dr McKay?" Woolsey asked.

"Firstly, I can alter the internal defensive system to detect nanites in the air. If they are detected the city will go into lockdown."

"Why do I foresee many false lockdowns?" John asked.

"Obviously by that stage whoever is behind it will have gained access to key systems and could have done other damage." McKay explained ignoring John.

"Is there anyway of detecting them if they are brought into the city?"

"Yes and no." Rodney said. "I have come up with a way to detect the ones in the air filters. It should be relatively simple to set up some scanners that will scan every piece of kit and every person that comes to the city. But it will only work if the nanites are active. If the Trust comes up with a way to have them completely deactivated when they enter the city there is nothing I can do."

"By nothing you mean nothing until your life is in danger?" John clarified.

"I mean nothing. The test involves picking up their RF signal, which is almost non existent anyway. It is like finding a needle in a haystack. If they are deactivated it would be like searching for an invisible needle in a haystack without touching the haystack."

"So you need a different test?" Ronon guessed, earning a scowl from Rodney.

"That was my take." John agreed.

"I'm sure you'll make that your top priority." Woolsey said looking at Rodney.

"Yes, fine. It is not like I have anything else to do. And I could give up sleep, I don't really need that."

"And food." Ronon added earning another scowl.

"Do we have any evidence that Milton was involved?" Woolsey asked, trying to bring the meeting back on track.

"No." Jennifer answered. "I had my team re-examine his blood work and scans. Neither showed any evidence of nanites."

"Matthews and Huntley both denied it." John added. "And he wasn't mentioned in any of the reports we found."

"Doesn't mean he's innocent." Rodney pointed out.

"True, but we can persecute him out of a personal grudge. Unless there is evidence the IOA won't act." Woolsey explained. "The SGC is well aware of our suspicions though and will be watching him." His last comment slightly appeasing Rodney. "Anything else to report?" He asked earning shakes of everyone's heads. "Good. Dr Keller, Colonel Caldwell, thank you for your time. I suggest you get yourself settled in. Colonel Sheppard I'd like your team to stay behind, you have been specifically requested for a mission tomorrow." Just as Jennifer was bout to leave Woolsey suddenly said. "Dr Keller, when we're done could you come back here? We need to discuss what's on the Ivangorod."

"You want me to stay behind now?" Jennifer asked.

"No. It is nothing serious, just something I thought would interest you on the manifest. Anyway the Ivangorod won't be within range for another hour or so and I'm sure you're looking forward to being back in your own clothes." He added noting Jennifer wearing slightly oversized BDUs.

Curious as to the news Jennifer headed down to her quarters.

-00-

"What're you doing out here?" Ronon asked walking out onto the balcony.

"Enjoying the view, fresh air and lack of walls." Jennifer smiled turning to face the Satedan. "And waiting for your meeting with Woolsey to finish so he can break whatever news it is. I take it he is free?"

"I'd give him some time. McKay ranted and ranted." Ronon shrugged.

"How much time?" Jennifer asked.

"Ten minutes, maybe twenty." Ronon suggested. "Want company while you wait?"

"I'd like that." Jennifer replied causing Ronon to walk up to her side.

"Ronon, I-" She started to say only to be cut off by Ronon kissing her.

"Dr Keller!" Hamilton exclaimed as he wondered on to a balcony, unintentionally interrupting Ronon and Jennifer's intimate moment.

"Dr Hamilton?" Jennifer asked confused, as she pulled away from Ronon. "What are you doing here?"

"I asked to come back, in an IOA capacity. I was hoping to learn from Atlantis. I took the Ivangorod across. Don't worry I'm not here to assess you or your team, I'm just trying to learn so I can take the best practices from here back to Earth. You'll barely notice I'm here." He smiled. "Anyway I should leave you to whatever you were doing." He added backing away. He was nearly back on the main corridor when he turned and said. "However, I feel I do have to mention one thing. You do realise that in your role as CMO having a relationship with any one posted here is wholly inappropriate." Hamilton said. "I mean-" He tried to continue only to find Ronon bearing down on him. "I should go." He added before backing off the balcony and disappearing down a corridor.

When Ronon turned back and saw Jennifer's expression he said. "I got rid of him. Without shooting him."

"Yes you did. At least I know what Woolsey wanted to discuss. But perhaps next time you could get rid of him without scaring him into firing me?"

"He deserved it." Ronon shrugged returning to Jennifer's side. "Besides I had other things planned than talking to the IOA."

"Really? Like what?" Jennifer asked. She was immediately answered by Ronon lacing his fingers through her hair and kissing her.

_-The End-_

**A/N:** Thank you to everyone for reading. I hope you enjoyed it.

Thanks again to daisyscrapper, whose last story gave me the idea for this one.


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